Fairly straight forward. I just got out of a very long fight against a Hegemony security fleet. Though wildly outgunned, we managed to pull out a victory against the glut of Onslaughts. In the end, although our loses were significant the enemy walked away with a single Piranha wing.
And... then the single ship Piranha wing attacked my fleet immediately after the first fight ended
. I was going to curb stomp him but sadly not a single ship of mine appeared in the encounter window and so most of my ships were captured. Again he attacked, finishing off everything else.
While I know it is a known issue that there's no warning when none of your ships are at sufficient crew levels to fight it was pretty infuriating to know that I still had a bunch of crew left and that if I didn't have the Apogee in slot #1 I could have easily fielded some ships.
If you don't have the option to field your #1 ship, it seems like the game should automatically promote the next ship down the line until you have something that is fully crewed. In my case, although I couldn't field my Apogee, I could have easily fielded the Medusa, Tempest and two Thunder wings. Since you need to define the order of your ships in the fleet deliberately to control how crew is split up, it seems like it's a safe bet the the first ship the game can find is probably something the player wants.
Having the option to re-order your fleet in the encounter screen would be nice as well.