Stone citadel not completed and says map failed

Ran the stone citadel, 0 enemies left, boss defeated and got a weathered crisis fragment, map would not complete and now says map failed. Maps connected past the citadel are now locked because the citadel cannot be reran.

Yeah, this seems to happen due to the Stone Citadel and Iron Citadel's bosses having second phases that use a completely new entity- the original boss seems to sometimes not be registered as "dead" and remains in the map, leaving it uncompletable. This presumably doesn't occur in the Copper Citadel due to Jamanra's second phase not using a new entity, just teleporting the first one to the new arena and changing his attack patterns.

I have personally found that I can avoid the issue fairly consistently in the Stone Citadel by avoiding clearing the map until after I defeat the boss. On the other hand, the Iron Citadel pretty much always has this issue for me- i've managed to avoid it once.

Usually, there are other routes around Citadels due to how city biomes generate, thankfully.