Looks like an opportunity to add our encountered bugs and shenanigans also!
Puzzles will sometimes stop letting you click the keypad, no matter how you do them.
We were unable to loot any items other than the crystals and commendations
Might be able to assist on that one. We found we could loot by passing who the op leader was to the person needing to loot their assigned item so had to pass it around a few times but it worked.
re: the actual encounter. If it was on hardmode you are doing it wrong. If it's normal I have no idea