This can happen if the boss is killed mid teleport as it registers the body as being in one place when in reality the bosses body is halfway across the mp. the normal fix is either walk through a door or relog if that doesn't work.
Joshua Doom- Imperial Templar
Mr Altmer- High elf sorcerer
Silent Destroyer- Khajiit nightblade
Heals-with-scales- Argonian Templar
Cat Sorc-- Khajiit sorcerer
The poison expert- Imperial Dragonknight
Templar Destroyer- High Elf Templar
Nooby Warden- High Elf Warden
Poisonous Noob- Redguard Dragonknight
Death-by-Magicka- Dark Elf Nightblade
Sinisterblade- Redguard Warden
Never tried rerunning back through the dungeon once completed so not really sure, but is there not a blue portal once you exit the molag kena area? If not, run back through the dungeon the long way and take the portal up to molag kena fight area?
You can't run back through the dungeon, the door past the Adjudicator is locked once the instance is completed. I think the blue portal will still take you to after the Planar Inhibitor, though... not quite sure.
Relogging would probably be the safest bet, so long as it doesn't punt you to the beginning of the instance.