In a letter to Engels of 14 February 1858, Marx says: “... As regards the ‘partisan style’, it is true that I departed somewhat from the tone of a cyclopedia. To see the dastardly, most miserable and meanest of blackguards described as Napoleon I was altogether too much. Bolivar is a veritable Soulouque (the former slave, later President of Haiti).”
The main source for Marx' opinion of Bolívar is an entry the former wrote about the latter in the New American Encyclopedia of 1858. The letter above on this entry shows Marx overall totally negative opinion of the libertador, comparing him to a leader of the Haitian rather than the french revolution - with the Haitian revolution and its violent liberation of slaves a "specter" for most white elites.
To it seems Marx has at least two main connected criticisms, one regarding corruption and one more generally on Bolívar's political stance: a) Bolívar argued against corruption while promoting it by keeping the traditional creole elites in power (pretty accurate). b) Bolívar evoked the French Revolution and republicanism while positioning himself as a dictator who wanted to rule over all Spanish America (it's more complicated than that). Let's look at those in some more detail.
a)
N.B. I've written some more about the development of corruption and sales of offices in Spanish America over here.
Marx' encyclopedia entry is really colored by his clear dislike for Bolívar. According to him, it seems the leader was a coward who just managed to win over large parts of Latin America from the Spanish because of the valor of his captains. I won't go into detail on this, but while he definitely has some points about Bolívar's military leadership I'd say it's quite an unfair and partisan portrayal.
On the other hand Marx criticism of Bolívar's stance towards corruption rings pretty true. As you mentioned, Bolívar did make various decrees against corruption - including one during the Venzuelan war of independence of 1812 that any corruption was punishable by death, and two similiar one during his presidency of the 1820s.
At the same time during the wars of independence the leader would order to plunder cities, and raise fund from often under-funded municipalities. Marx in his entries talks about such instances, e.g. when early on in 1810
Bolivar marched toward Pamplona, where he spent about 2 months in festivals and balls. Nov. 3, he arrived at Montecal, in Venezuela, whither he had directed the patriotic chieftains of that territory to assemble with their troops. With a treasury of about $2,000,000, raised from the inhabitants of New Granada by forced contributions ... [he encountered the enemy].
Marx gives more such examples, but the overall criticism goes deeper: Bolívar was clearly a member of the "burgeois" (for Marx), ie creole elites of Venezuela. Instead of initiating a republic with the citizens' participation, under Bolívar (and other revolutionary leaders) the creole elites would stay in power in many parts of Latin America. This meant that the large-scale corruption developed througout colonial times would continue and often increase, with no more Spanish officials as "middle men". So that in some ways, the revolutionar leaders can be seen as preparing the ground for the caudillo (or "Strongman") political leader type who would dominate Latin American politics arguably into the 20th c. While it's too easy to just make Bolívar responsible for the wide-spread modern-day corruption in Venezuela and other L.American countries, he and other leaders certainly paved the way by maintaining the traditional elites' influence.
b)
I've already written in more detail about Bolívar's political views over here, so will keep this part a bit briefer by building on that.
In the entry, Marx describes how Bolívar managed to become "dictator" following the successful wars of independence by fixing his powers through law. Commenting on the latter's plans to build a Pan-American union in 1826, according to Marx>
What he really aimed at was the erection of the whole of South America into one federative republic, with himself as its dictator.
As mentioned in the beginning, Bolívar's political views were complex and changed over time. His sejourn to Europe and witnessing the crowning of Napoleon had left him with an admiration for the French Revolution and especially for Bonaparte. The French constitution was routinely formed the basis of many constiutions of the newly independent South American nations; while U.S. independence surely served as another example, Bolívar and other leaders were more wary of possible U.S. influence in the region. Lastly, while the Haitian revolution may have served as another template, since many of the creole elites were actually slave holder they were in many ways afraid of the Haitian example. What is more, Bolivar's stance towards slavery was similarly complicated: he promised liberty for slave soldiers participating in his campaigns, while continuing to hold slaves himself.
So to put it more simply, Bolívar definitely started out with republican ideals and admiration for France. Over time though, he became more influenced by ideas of having a strong leader (ie himself) in power. At one point he even entertained the idea of having a sort of constitutional monarchy with Britain serving as arbiting power - which of course didn't sit well with other revolutionary leaders. In part, Bolívar's changing position can be connected to a certain resignation vis-a-vis his own deeds and waning influence. Towards the end of his Bolívar had seen the failure of many of his initial political ideas, including of a Pan-American union. While we can see an increasing tendency for him towards having a "strong-man" ruler and/or constitutional monarchy, this was at least partially grounded in the failure of republican and pan-american projects.
Summing up: In trying to get at Marx parlance, we could maybe say that for him Bolívar squandered the revolutionary potential of the wars of independence - or that rather than helping to unleash the revolutionary potential of the lower classes in a true social revolution, he went towards the idea that they should be protected from the elitist congresses by an enlightened dictator: himself. I've looked at some valid criticisms of Bolívar, e.g. his ruling against corruption and slavery while continuing the practices at the same time.
Stepping a bit back, it seems to me that Marx' views overtly color his negative views of Bolívar. After all, we're talking about larger practices of corruption that had developed over centures in colonial Spanish America. And about a creole elite that had been the prime instigator of the revolutionary wars, who wanted to gain more power from the Spanish colonists - and whose main motivation was of course to stay in power. So to simply blame Bolívar's dictatorial impulses for all this simplifies a) his political views and b) the longer socio-economic processes that the revolutionary wars formed part of.