So if a player makes an illegal placement and everyone misses it until end game scoring what do you do?
As far as I can see there's no penalty or mention in rules if someone does it either by mistake or deliberately.
From the last page of the rules:
"If an offending tile is found only during final scoring, it is too late to correct the mistake. Complete scoring normally, including the offending tile."
"When a player places a terrain tile incorrectly, first apply the rules mentioned above. In addition, the offending player loses a prophet which is permanently removed from the game. If a prophet was on the offending tile, that prophet is the one that is removed from the game"
So the tile remains and any prophet on the tile is removed.