One thing that always bugged me was how if you get a save during the BioLabs map and you quit the game, when you return all the enemies will have respawned. This is the opposite of all the other maps.
Also, once you reach, I believe, the R & D map, when you quit the game (after any save) and you don't have full health, you'll end up with just a small amount of health when you return. Also is you have any over-health from a buff, that is also lost. Basically you'll start with a small amount of health or full health. Nothing else.
I've played this game quite a lot. Two separate New game+ play-throughs @ core level 270+ on each. So I can tell these are strange occurrences.