Even the chests in normal flashpoints while leveling up bug out and you are unable to interact with them after killing the boss. Happened to me two times in the same Boarding Party run last night. Its disappointing to finally get a group on the same page and kill a boss and then get no loot for it.
To loot the chests in Boarding Party (Heroic and Normal) you have to kill the boss very close to the chest. We killed em on top of them. Good to know next time your in there with your crew.