If any such sects ever existed, they would have been very tiny and on the fringes, doomed to fall apart quickly. This is for a simple reason:

The fruit never was an apple.

The actual texts only say "fruit," and don't specify beyond that point. Given that the Jewish religion from which Genesis arose was a Near Eastern religion, if a particular fruit was in the mind of the author, it was unlikely to be something relatively alien to the region, and especially the Mesopotamian region in which Eden is placed by the text.

So where did the idea come from? It's derived from the Vulgate translation of the Bible into Latin by St. Jerome in the late 4th century. The Latin word for an evil thing is "malum." Coincidentally, the word for an apple is "mа̄lum," and all the forms of these words are very similar. Thus, the latin phrase "ligno autem scientiæ boni et mali" could be (mis)read two ways:

• the tree, however, of the knowledge of good and evil
• the tree, however, of the knowledge of good and apple

Educated individuals in Western Europe generally knew well enough to not get confused here, but the humor here was not missed by poets and artists, who picked it up and ran with it. Since Christianity has generally been friendly to local adaptations so long as they're doctrinally orthodox (see depictions of Jesus or the Virgin Mary in different cultures), there was little objection to putting this spin into the imagery, and it's stuck around in the Western European imagination since.

There was, however, a related phenomenon in some sects of gnostic/dualistic Christianity who interpreted Genesis very different (according to most of our sources, which are admittedly hostile). Instead of this fruit being an instrument of evil, it was often seen as a instrument of liberation which gave the secret knowledge necessary to free the soul from material bondage.

Accordingly, the consumption of fruit, especially clearer fruits like pears, was encouraged. This is part of why Augustine, who dabbled in Manichaeism, makes such a big deal in his Confessions about having stolen pears and discarded them. These particular sects, however, did not flourish for very long, and later incarnations of Christian gnosticism (e.g. Catharism or Bogomilism) do not appear to have carried on this tradition.