In UAC Aerospace Lab mission, the final enemy(ies) surrendered and I was moved to the underground phase. However, no equipment (either on the craft or from the enemies) transferred on that stage, so even though I got the chance re-equip the squad, the pool to choose from was empty. There was also no loot pile to equip from anywhere on the floor, as there always has been on multistage missions.
This is likely a bug, but it seems so strange that I have no idea where. Sorry, I didn't save before the first part ended.