It's that locked Fracture-like debuff (in this case, it's named Decommissioned). If a non-summoned ship gets to 1% health and protection, it goes back to full hp+prot (unless it has healing immunity or the debuff from Profundity that prevents healing), and the moment it takes a turn, it's destroyed. You can looked at the full description on the Bracca screen when you select the fleet mission. It's the green icon in the "abilities affecting territory" section.
If you mean your ships died before/without getting the debuff, then yeah, that's most likely a bug.