All ships belonging to a race with the Promethion Born Ability do not repair like other ships. They can only repair when in a fleet with right type of commander ship, and the commander ship uses promethion to repair all ships in the fleet.
The Onyx Hive have the Promethion Born ability, and their commander ships have the ability to use promethion to repair all ships in their fleet.
It looks like you're playing as a custom race and have the commander ships from the Cosmic Contaminate. I guess the custom race has the Promethion Born ability, which keeps them from healing. If all this is true, your ships will never heal.
