Well, here's the plot holes that just jump to mind...
They are spoilers. Don't read if you haven't seen the movie.
'It flows from the source'; again, completely unexplained
A metal machine passess through Neo. In the real world. In a spaceship. Just flies through the windshild and him. WTF?
The super-powerful machine city has antiquitated defense systems that can't even shoot inside... what? Furthermore, the ship just happens to crash at just the right place in this massive city.
This has been mentioned a lot other places because it's so ridiculous... Trinity gets SCEWERED by a number of metal beams in the stomach and chest. She would been dead or in a coma in seconds from blood loss and, well, her internal organs being ruptured, and her last moments would be spent screaming in pain. But no, she has time for this long, dramatic death scene...
Neo is caught between the machine world and the real world-- how? His connection with this Deus Ex Machina 'The Source' has somehow linked him into the Matrix when he's not even at broadcast depth? The train station may be a decent philisophical analogy, but it dosen't make a scrap of sense plot-wise.
Both movies are full of guns that fire way more shots than their clips can hold without reloading.
Well that's all I can think of
. There have been more mistake-filled movies, surely, but I can't think of any offhand with such a massive budget and such a thin plot.
--Mouse: Famous (Avatarless) Fighting Furball
A very nice %it, indeed.