I had an issue with the gate after it blows open my crew kept getting hung up on the sides that remain after the middle part vanishes. I had to move in and out of the gate a few times to get them to follow me.
on the first cut scene, when the warbird de-cloaks, you dont get the cloak visual. it just sort of fades in. all the other cloak animations work just never for the warbird.
also when you speak to obisek and make your choice, two of the boffs tend to get transported about 100m away. getting killed and re-spawning will get them back but it happens mots times (if not every time)