I've seen a similar problem. It doesn't always take saving and quitting, though. Sometimes it happens while going to a new loop. I ended up with the beefiest gheist to ever beef with no food and using the bad fusion. Items had little or no hp bonuses either. Was weird and difficult to try and make him my lowest health since I wanted him to be targeted most.
Another bug/problem I think I might have found is that percentage buffs to healing don't seem to actually be working. I'm not perfect, so it's entirely possible my math was off every time or that I misunderstood something, though. The nature synergy buff, and any item buffs didn't seem to be doing anything though.