Well, here's another one; when they're all having the conversation about why everything tastes like chicken -load of crap. I quote (not accurately) "Maybe they didn't know what to make everything tase like...and that's why everything tastes like chicken"
The reason things taste as they do is because of the chemicals in the thing in question.

Another flaw; why go in to the matrix and risk your neck when you can just program an army to do all the dirty work for you?

Yet another flaw; why do they give a damn if they are in the matrix? The real world in that film is crap.