It would have to subvert the "can't create negative memories" somewhat, but I think the easiest explanation is that Mr Poopy Butthole getting shot was itself a false memory, by the same parasite as Mr Poopy Butthole. Note how we never see him die. Maybe it's a setup to him forgiving her later, and thus becoming a trusted and no one suspecting a parasite.
Yeah, so great.
watch the after-credits scene