I've had an issue where of my ships in a fleet only one would actively engage in combat. while the others stayed out of range for most of the fight. The problem turned out to be that I had a missile boat classified as support because I wanted it to stay back and fire missiles at long range. (That's how I read the description). The two other ships were free spawns (malevolent frigate and a small ship from a survey) and since those start as escort they would stay out of the fight as well.

The problem with upgrading was that the rocket boat used my only antimatter resource so a different classified identical design didn't show up as an option and upgrading twice seemed kind of expensive. The freespawn ships came with railguns which I hadn't unlocked yet and in the case of the frigate were a bigger size than I could build myself.