edit - whoops, misread your post.
On topic: I think one of the worst films for plot holes must be Star Trek: First Contact. If you think about that film for one second your head explodes in a mess of contradictory plot devices, gaps, mishaps and utter nonsense. Trek films never make sense, but even by Trek standards the eighth movie is downright loony.
Stranger than the plot hiccups of Star Wars (the prequels in particular) are the people who write lengthy essays in an attempt to 'explain' inconsistent garbage. The depths to which they will distort and convolute basic facts and reasonableness in logic is quite weird and disturbingly obsessive. Almost fascinating, maybe.