Happened here too.
I was running T3 vault bounties, completed one bounty, started a second bounty and the first stage was the mist fissure. Activated the nearest rift and killed the spawns but it never sealed. The timer ran out and I repeated about four times with the same fissure and a different one. They both failed to seal each time after eliminating enemies and the timer reached 00:00.
I aborted the bounty, returning to the surface, and looked for a thread on this bug. One suggested waiting until the timer reaches 01:16 before killing the spawns to allow them to finished spawning