In the Malleus Maleficarum, Kramer and Sprenger refer to "the observing of times and seasons" as a superstition. What is meant by this?

Admittedly Kramer was not very good with theology, and for that Malleus was disavowed by the Papacy. Nonetheless the methodology is enlightening. We can use this phrase to show how medieval inquisitors and demonologists did their work.

The Malleus Malificarum is a manual structured like many inquisitor's manuals were, composed as general questions which must be tested in order to conclude there is witchcraft. In this case, the phrase you mention is in Part I, Question II^1:

Question II: If it be in Accordance with the Catholic Faith to maintain that in Order to bring about some Effect of Magic, the Devil must intimately co-operate with the Witch, or whether one without the other, that is to say, the Devil without the Witch, or conversely, could produce such an Effect.

Prior to the 15th century the 'witch' did not exist to the Church - she was in fact for centuries before a fiction and belief in that fiction by a Christian was actually punishable. The context of how the witch developed tells us something about what Kramer was saying.

In the 13th century the Church was deeply involved in persecuting those it viewed as heretics. Those first inquisitors put together a number of manuals for inquiring into and testing heretics. Progressively through the 14th century 'sorcery' (maleficum) became a subset of heretical investigations (although not all inquisitors agreed to the existence of sorcery). By the mid 15th century, the time of Kramer's Malleus, the witch had been constructed by ecclesiastics welding together numerous folk beliefs and intellectual (theological) theories of demons.

The key component of the new witch-as-heretic was the witch's interaction with the Devil; if there was no interaction with the Devil (in whatever form), she was not a witch and not a heretic. This required fairly precise understanding of what did and did not constitute interaction with the Devil. I think we can see then why Kramer's question is important: he wants to test evidence of the work of/with the Devil.

One of the flash points in demonology since the late antiquity was divination, or foretelling God's plan. The Bishop Isidore of Seville's formulation of magic and divination in the 6th century pretty much became standard text for the Church:

Isidore of Seville (ca. 560-636), borrowing from classical authors such as Varro (ca. 116-ca. 27 B.C.), listed geomancy, hydromancy, aeromancy, and pyromancy (divination by earth, water, air, and fire) under the heading "magic," and then went on under the same heading to discuss divinatory observation of the flight and cries of birds, the entrails of sacrificial animals, and the positions of stars and planets (i.e. astrology). Only after cataloging these and other species of divination did he include enchantment (magical use of words), ligatures (medical use of magical objects bound to the patient), and various other phenomena in his discussion of magic. "All such things," he said, "involve the art of demons, which arises from the pestiferous society of men and bad angels."^2

But the Church's position on divination was a bit complicated through out the early middle ages, partially because 'magic', 'sorcery' and beliefs in 'witches' were, following Roman law, considered a secular issue and only punishable when a crime (murder, injury, theft) was involved. So, ecclesiastics didn't think much about it, and because of that we have little records to show for it. The other complicated issue was that the Roman Church held that witchcraft just didn't (couldn't) exist (see the link above from the capitularies of Charlemagne which became canon law in 10-11th century).

By the 13th century, two things happened:

Theologians began to wed demonology with heresy, and heresy was definitely (although not exclusively) Church jurisdiction. Demonology became a significant area of concern and inquiry for the Church. The writings on the subject suddenly spike as of the 1220's.
Divination came under scrutiny, but was not entirely found suspect. As 'natural philosophy' arose in the new universities we see the separation of 'magic' and 'natural philosophy'. This was a thorny division as there was not perfect agreement on the divide between the two categories. One example of this debate was the place of astrology. Some theologians held that astrology was summoning demonic magic for purposes of intervening in God's order; others held that it was effectively a science that simply read the 'language of stars and planets' set forth by God himself. The latter belief became the dominant thinking and permitted kings, queens, popes and bishops to dabble in astrology themselves.

So, now we have some tools to examine Kramer's passage. He iterates through superstitions for the presence of demons, for work with or on behalf of demons. Here is the full passage:

And because these and many other charms like to them may be placed in the third category of superstition, that is to say, idle and vain observing of time and seasons, this is by no means a relevant argument as to the heresy of witches. But of this category, the observing of times and seasons, there are four distinct species: A man may use such observations to acquire certain knowledge: or he may in this way seek to inform himself concerning lucky or unlucky days and things: or he may use sacred words and prayers as a charm with no reference to their meaning: or he may intend and desire to bring about some beneficial change in some body. All this Saint Thomas [Aquinas] has amply treated in that question where he asks, Whether such observing be lawful, especially if it be to bring about a beneficial change in a body, that is to say, the restoration of persons to health. But when witches observe times and seasons, their practices must be held to belong to the second kind of superstition, and therefore, in so far as they are concerned, questions concerning this third class are wholly impertinent.

The passage is frustrating (like most inquisitors' manuals) because its not actually a list of what constitutes a heretical belief. Kramer here, as was inquisitor practice, is always holding open the possibility that anything could be heretical depending on the intent and the impact. The notion of 'time and season' has to be calibrated to the middle ages and so Kramer, invoking the lessons of Saint Thomas Aquinas, gives the all clear to 'idle and vain observing of time and seasons'; we can infer here that he means various peasant beliefs about when to plant crops, perhaps marginal prayers to be said at a given time in hopes that God hears them, or appeals and gifts for a saint for intervention based on a particular feast day, maybe even an augury through the formations of migrating birds. Kramer treats these as a 'third category of superstition' which is effectively a harmless appeal to God's order of things.

But the referral to 'time and season' is important for another reason: studies of witch hunting and demonology have noted that the witch (and heretics) created by witch hunters are perfect inversions of Christians and Christian observances^3 . For every altar to God, witches have altars to the Devil; for every Christian mass, there is a black Satanic synagogues; for every eucharistic wafer, drink and kiss, there is an offering to the Devil, his penis and his ass. Witches were said to celebrate their evil sabbats on exactly those days Christians might celebrate. And so it goes as though mocked in some blackened mirror.

So it is then that Kramer turns to witches in the same breath, warning us that the witch's observance of time and season is important. He is calling for shrewdness on the part of the inquisitor in paying attention to the difference between witch and Christian, because, following another common trope of inquisitors, the heretic will try to fool the mind of the inquisitor, masquerading as Christian.

In the following paragraph he holds that the 'observances of witches' adhere to a 'second class of superstition': 'divination'. He defines divination as:

the operations of which are performed by express and explicit invocations of the devil; and this may be done in very many ways, as by Necromancy, Geomancy, Hydromancy, etc.

He attempts an appeal to Aquinas so as to point to extra-text guidance regarding what may be 'harmless' or may have already been cleared by the Church as 'natural philosophy'. So Kramer goes on to say:

Let us therefore only consider Astrology. In Astrology there is no compact, and therefore there is no invocation, unless by chance there be some kind of tacit invocation, since the figures of demons and their names sometimes appear in Astrological charts.

The inquisitor is thus instructed that 'observance of time and season' must be scrutinized according to certain categories with a careful sifting of the evidence which may be the Devil's attempt to conceal itself: the Christian light may in fact be the blackened mirror.

^1 for easy of copypasta I am using the freely available Montague Summers edition; it's now discredited as a translation but for purposes here it's sufficiently accurate.

^2 Kieckhefer, Richard. Magic in the Middle Ages (Cambridge University Press, 2000)

^3 See Norman Cohn on this particular aspect in Europe's Inner Demons: The Demonization of Christians In Medieval Christendom (Random House, 2011)

They explain what they take issue with. Quoting the translation by Montague Summers:

Wherefore this divination, which is used when they are working their spells, must be judged to be the height of criminal wickedness, although some have attempted to regard it from another point of view. And they argue thus, that as we do not know the hidden powers of nature, it may be that the witches are merely employing or seeking to employ these hidden powers: assuredly if they are employing the natural power of natural things to bring about a natural effect, this must be perfectly lawful. as indeed is obvious enough. Or even let us conceive that if the superstitiously employ natural things, as, for example, by writing down certain characters or unknown names of some kind, and that then they use these runes for restoring a person to health, or for inducing friendship, or with some useful end, and not at all for doing any damage or harm, in such cases, it may be granted, I say, that there is no express invocation of demons; nevertheless it cannot be that these spells are employed without a tacit invocation, wherefore all such charms must be judged to be wholly unlawful.

And because these and many other charms like to them may be placed in the third category of superstition, that is to say, idle and vain observing of time and seasons, this is by no means a relevant argument as to the heresy of witches. But of this category, the observing of times and seasons, there are four distinct species: A man may use such observations to acquire certain knowledge: or he may in this way seek to inform himself concerning lucky or unlucky days and things: or he may use sacred words and prayers as a charm with no reference to their meaning: or he may intend and desire to bring about some beneficial change in some body. All this S. Thomas has amply treated in that question where he asks, Whether such observing be lawful, especially if it be to bring about a beneficial change in a body, that is to say, the restoration of persons to health. But when witches observe times and seasons, their practices must be held to belong to the second kind of superstition, and therefore, in so far as they are concerned, questions concerning this third class are wholly impertinent.

(II q.2; Latin text, bottom of the page starting with Ideo haec Divinatio Maleficorum.)

My interpretation is as follows:

Some people do indeed argue that observing the seasons is a (3rd) harmless form of divination.
Thomas Aquinas provides a nuanced view on the general matter in his Summa Theologiae (II II q.96 a.2).
But, mind you (puta), Thomas only talks about beneficial effects (ad sanitatem). The observations of witches (observationes Maleficorum, literally: "observations of evildoers") do trivially (it's in their name...) not fall under this category (hinc locum non habeant).
Therefore (ergo) the "Thomist" argument that everything is fine as long as natural means are used to produce natural effects does not apply to witches (note the subjunctive: hoc licitum foret, ut de se patet, the Malleus has just been referring this view and never adopted it, the English translation misleads).
Indeed Thomas' concept of tacit pacts (tacita pacta) which he applies to astronomical/astrological observations has to be extended to everything in this area that witches do (cf. licet non absque tacita ista [invocatione] fieri possent), even if it may superficially appear as beneficial (e.g. pro acquirenda sanitate, ad corpora immutanda in melius). With witches demonic forces are always supposed to be at work.

I'm by no means certain of this interpretation. Just compare the two places (Malleus and STh). With Thomas you may or may not agree but you always know what he is arguing and with which reasons, the Malleus betrays the intellectual level of its authors even in form.