Quests from one playthrough carrying over to another

I’m playing 3 different characters at the moment. FL4K when by myself, Amara with my husband and Moze with my son. Last I played with my son and we’re in Lecra City in Promethia, I noticed that we’d picked up a battery and killed one of the main NPCs but I was pretty sure we hadn’t actually done those in our previous play session; I’d done it with FL4K earlier in the day.
Today I started up FL4K and found that the quest with the guy locked in the toilet was showing as done to the point of finding him after the loo had blasted off. I only picked up that quest with FL4K yesterday, but got to that point with my son and Moze so it looks like my single player game is picking up info from the co-op game and vice versa!