I'm looking for historical examples of logical fallacies (may be formal or informal) made by philosophers. Preferably as uncontroversial as possible.
Immanuel Kant has a principio principii, or begging the question, in the last chapter of his Critique of Pure Reason. This example is rather uncontroversial, because it has been pointed out (or hinted at) in a review of the A edition by Christian Garve and obviously it has been acknowledged by Kant himself (suprisingly, he did not alter this chapter in his B edition, though).
He comes from the fact of a moral law, going to the object of a will under it (the highest good) and the ideas of God and an immortal soul. But only given God and an immortal soul, he claims then, the moral law is even effective for the will. Freedom (in the guise of a will under a 'pure', a priori law) and God, here, presuppose each other.
It is in the original review, not the one posted in the Göttinger Gelehrten Anzeigen, which was mutilated by Feder. Kant received the original in late 1783 and realized that fallacy, some even tend to claim that it was one of the main reasons for writing the Groundwork and, in effect, the drive that led to the other two critiques.
This is depicted in e.g. The 25 Years of Philosophy by Eckart Förster:
In the dialectic Kant had, on the one hand, shown that we cannot know anything about God and that theoretical cognition of supersensible objects must be ruled out as impossible in principle. On the other hand, he argues that certain propositions of practical reason cannot be true, or rather, cannot motivate action unless we can assume the existence of God and a future life. It is thus the validity and obligatory force of the moral law itself which reintroduces God into theoretical cognition, while at the same time it is the idea of God which serves to explain the bindingness and validity of the law . For “reason finds itself constrained to assume” the existence of God, Kant writes in the Critique, since “otherwise it would have to regard the moral laws as empty figments of the brain” (A811).
Kant is thus guilty of a petitio principii which only becomes clear to him through Garve’s objection (for the published version [i.e. Göttinger Anzeigen] of the review had passed over this point as incomprehensible). His explanation presupposes the very thing it is supposed to explain. (The Twenty-Five Years of Philosophy, p.52)