Since it was partway through the mission I'd ended up with a full inventory, as you do. Usually when you go to pick something up with auto loot on it won't pick it up but the option to pick it up will remain. So you can exit the window, discard something and then click take items again. You cannot discard an item and pick it up from the existing window you have to close it then select it again.
It didn't give the option again but the accolade still triggered so the crystal is considered obtained and trying the mission again doesn't have the item as interactable. If any staff member can help it was on Slavicus that it messed up. I'd really like to get the crystal please.
good luck on getting this fixed. They seem to have keyed the lobi to the accolade so people wouldn't be able to go farm them. I have seen other posts where this has happened to others, so you are not alone.