My friend and I were playing co-op for System Shock 2. Everything was fine with the first play through today. When we reached a certain point in the game we stopped and saved. When we came back to the same saved state, it was corrupted. My friend was hosting the whole time so we were using his saves. Course, we both saved around the same point like always so we had a backup.

First thing to happen and I'm quoting my friend on this "When I spawned, it spawned me in the same spot but you were at the beginning of the map and to the left of me were containers of the same items as my friends". Meaning that somehow some of my items from my inventory duplicated.

Next thing to happen was that my friend also gained a large amount of nanites (or in game money) at random. then a bunch of other random crap happened. So all in all the saves are ruined.

Is there possible way to either fix this or make it so this doesn't happen again?

unfortunately, no. all you can do is save often and have a lot of patience.