There are a couple that come to mind for me and the first one is Super Metroid. If you make it to Tourian, I dont believe there is any way to go back to the other areas to get all the items once you save in there. So you have to make sure youve gotten everything up to that point.

Another is Grand Theft Auto 3 and possibly its sequels. I remember a part where if you go straight to the last mission on the first island and beat it, the other uncompleted missions disappear from the map.

Im playing Donkey Kong Land right now and it seems there may be a similar thing where if you skip a level, you cant get 100%, but I wonder if that means you can still go back and beat it to get 100%