The most obvious problem is Thucydides' admitted habit of making up speeches for people to give. While, in some cases, it's speeches he would've personally witnessed, like Pericles' Funeral Oration, and thus would at least reasonably be somewhat close to what Pericles actually said, in other cases, he's sticking lengthy speeches into the mouths of Spartan and Athenian ambassadors to Corcyra with no reason to believe that they said anything similar to what is put in their mouths.

Thucydides also has a severe axe to grind with the populist/democratic faction in Athens and, while it is hardly rare for historians to take sides when describing events, his close relation to the events in question makes his blackening of certain figures' reputations a bit eyebrow-raising. He knew Cleon, Alcibiades, and the rest personally and his hatred of them would definitely look bad in a modern historian.