Episodes I and II introduced more plot holes to the Star Wars saga than any other Episode. I can't tell you exactly which holes, but they're there (and a lot of them too). Unfortunately story incosistencies have been removed from the Internet Movie Database until Episode III has been released.
In Episode V on the ice planet Hoth, shortly before Luke is rescued by Han Solo, Obi-Wan Kenobi appears before Luke instructing hime to go to Dagobah to be trained by the same Jedi master who instructed him. Later in the movie Luke receives his training from Yoda. In Episode I however we learn that Qui-Gon Jinn is the instructor of young Obi-Wan Kenobi.
This plot hole had to be corrected by GL and he did. In Episode II we see Obi-Wan entering a class at some sort of Jedi training centre and we see Yoda teach very young children the ways of The Force. We're meant to assume that this is where Obi-Wan received his first training as a small child too, prior to being appointed the Qui-Gon Jinn as a Padawan Learner.
During his second visit to Dagobah in Episode VI, Luke is told by Obi-Wan that he (Obi-Wan) "took it upon himself to train him as a Jedi" (refering to Anakin Skywalker), thinking he could do this just as good as Yoda. In Episode I we see Qui-Gon Jinn being the one who does just that. Obi-Wan Kenobi only takes over this 'job' reluctantly after Qui-Gon Jinn has been killed at the end of Episode I. Not exactly the way Obi-Wan told Luke (and us) the way it all happened. Maybe the conversation in Episode VI will be changed in the upcoming DVD to match the events in Episode I.
This is one of the reasons I disslike the updated and altered versions of the Original Trilogy. They are fine the way they are. All changes made to these movies are either cosmetic and as such are only meant as eye candy, not adding anything to the story, or they are meant to cover-up plot holes that were introduced in Episodes I and II. If he had watched his Original Trilogy more carefully before writing the stories for the prequels, he wouln't have to correct these unnecessary plot holes afterwards.