It also saves your progress through the mission.
You must have been in the ninja turtles area where my copy crashed. I had to go all the way through it again also, but my mission progress was saved.
Am I right or were you in a different area?
No, I was in the animal preserve. It really hated me there (at least when I went into menus). Every single time it crashed it spawned me at the start (and from what I remember when you start up the game from scratch it spawns you at where the travel station is, least that's how mine acts. Not noticeable in open worlds cause you don't have some goal of getitng to the end, but stuff where they design it like a dungeon you have to find the end of, it sucks when it crashes).
It crashed on me when I was more than halfway through (just had one more area to clear really). Had to redo it all. It crashed on me after I killed the bird and had just opened the safes in the room after and when I re opened the game it respawned me at the beginning. And I think it might have crashed one more time earlier but it was so much towards the beginning it wasn't a huge deal so I didn't pay attention.
Oh, and I'm not the person who said he had to re run the dungeon three times. I am just affirming his statement that yes, it happens (and as far as I know the game is designed not to remember where you were and spawns you at the save point that you can travel from in each area. At least that is how it works for me every time I open the game from when I quit it or it crashes).
The only thing I've seen it use the non travel save points is for if I die I spawn at the last one. But not if I quit the game or the game crashes. It always spawns from the travel point in those cases. Which in the dungeons/missions, is always at the start.