I didn’t look at it as so much of a plot hole, but the first clue that when you’re in the “real world” you’re not actually in reality but really still in the matrix (or perhaps another matrix that doesn’t work quite the same). Same thing with the whole scorch the sky bit - doesn’t make sense in reality but in a simulated reality you can change up the rules a bit. The second movie, to me, played into this further with a bunch more clues dropped about that what the characters considered reality wasn’t actually real. The third movie, obviously, would deal with that… but instead… well I’m still not sure what the hell that movie was about.
I didn’t look at it as so much of a plot hole, but the first clue that when you’re in the “real world” you’re not actually in reality but really still in the matrix (or perhaps another matrix that doesn’t work quite the same). Same thing with the whole scorch the sky bit - doesn’t make sense in reality but in a simulated reality you can change up the rules a bit. The second movie, to me, played into this further with a bunch more clues dropped about that what the characters considered reality wasn’t actually real. The third movie, obviously, would deal with that… but instead… well I’m still not sure what the hell that movie was about.
Yeah that would have been a great way to fix their problems.