Ok, so after completing the quest in Hydroponics, I tried to go to the Med Sci deck before meeting Dr. Polito. It spawns me in the wrong place, first near the energy charger guarded by two turrets, after a while in the black void from where I can see the entire level while falling down. It looks like I do have some dmls but they aren't working. Here's a relevant save, by the way: save file

some more info would be nice (mods used, for example), but yeah, looks like a gamesys/map mod has been activated mid-game. dmls can't really break the game in such a way.