If weapons are drawn, it creates a crime scene in the vicinity that friendly/neutral NPCs react to. There may have been a problem with the end of the combat, which the next(?) combat cleared. It seems the issue isn't exactly the same as previous cases, if unsheathing and resheathing weapons didn't help, though.
The issue with the Kraken summons was brought up with the design team during development, and they were fine with it as it is. If your characters agree to be purged at the end of the game, they will also be brought back (with a brief explanation during the cutscene) and be present for the epilogue section.
