Ah I think I found the issue with the bird. she's meant to fly back behind robot but an oversight got her stuck in the wall with the game waiting for her to move to the position. I've found a fix for it.
Re: the battle with Wendigo I tried it out and it completed it. After he transforms and turns dark, there's a skill that gets added to your skill set called Deus, did you use that against him?
Anyway I've made a new version and did a bit of a blitz through the main story and checked the Tower of Trials entrance. I'll get it uploaded.