Speaking of April, it's gone for me now, but for a while you could find Rick in lover's bridge which leads to a cutscene with invisible April and a boss battle that leads to a black screen. Don't do it.
Another issue in the underground is being unable to complete Patricia's quest if you get to Damien's room after saving him from V and you already started the quest without completing it.
EDIT: To be fair these sorts of glitches existed even without old save files on a new version. Like for example, if you went to the hospital after Lavender's mission to escape from there you randomly had her prompts. Similarly now going to the nightmare realm will have Aelita speak even if she's not there.
