Important note: Ship Size Restrictions!
Due to the current restrictions in Arena Commander, certain larger sized ships will not be able to be used and players will instead be granted secondary loaner to allow their owners to play in all game modes. For example, Constellation owners receive a Hornet for use in Arena Commander play modes.
This is not a bug and is intended. Check out the Loaner Ship Matrix to check if your ship is not currently available for use in Arena Commander.
Other Possible Rare Issues
After filing an insurance claim on your ship in the PU, you might enter Arena Commander to find that your ship is now missing from your available options. This is a known issue that we are working to resolve. In the mean time please report this situation on the Issue Council with as much information as possible so that our teams can investigate properly.
To resolve this, you will need to perform a Character Reset. We recommend only taking this step as a last resort.