I distinctly remember a situation where a certain character that originally died had escaped death for seemingly no reason when I got different endings. It's been a while since I've played it, but that stuck out to me as being a real "What are you trying to pull, game!?" moment. Though I haven't played VLR, so maybe they explain it in some crazy pseudo-science-y way later on in the timeline. Maybe Mantorok had something to do with it.
@Anjon said:Events shift in 999 when they really shouldn't. For example, there's a character who can die if you choose a certain course of action, but that action has nothing to do with them nor how they die. It's just an arbitrary change much like Heavy Rain's arbitrary changes.
I got every ending in 999 and have no idea what you're talking about. Your path opens up situations for certain things to happen that wouldn't in other storylines, but there's never an instance where something happens in one playthrough that should've happened in the others but didn't, at least not that I can remember.
Apologies for incredibly obscure references.