9. The Matrix
The Hole: Why Does The Matrix Allow Free Thought?
More of a logical query than a gaping plot-hole, but the decision by the Matrix's machine over-lords to make the captives of The Matrix capable of free thought (and thus protest) seems to have been something of a mistake. If they have the capabilities to build that sort of system, and basically pull the wool over the eyes of an entire civilization, why didn't they have the fore-thought to manipulate their brain function even more to stop them from questioning their existence?
That would presumably have stopped all of the escapees before they ever enjoyed their epiphanies.
Even better, why didn't the Matrix just create a simulated universe without computers, so Neo could never have been found by Trinity? Why not drop them all into 18th century rural Spain where they wouldn't have the capabilities and could be controlled a darn sight easier?
But we didn't seem to care when the first Matrix film came out, and we were all apparently willing to accept such a ridiculous premise, because the sci-fi stood up so well: it was only when the poor, messy sequels arrived that people started to pick away at the stitches, and even then those concerns largely targeted the problems of Reloaded and Revolutions.