The Avernus command ship is supposed to heal 100% after each battle (which it usually does), but after attacking a Manti shipyard, it did not. The following screen snapshot shows that the hit points are only 24, but should be 96. The fact that moves available are 12/12 proves that I am at the beginning of the next turn.
I have uploaded a save to DropBox that should allow you to replicate this issue. The save is located here:
After loading the save, select the Avernus-1 ship, then use it to attack the Manti shipyard.