I don't know if this is related...
My current Scavenger ship has a Raider Bay (lvl 37) and an Interceptor Bay (lvl 35), so my ship has a swarm of 7 ships (4 raiders, 3 interceptors). I recently found a Bomber Bay (lvl 36), which I swapped for the interceptors. I could only launch 5 ships in total (4 raiders, 1 bomber).
I could launch a normal number of bombers, but the raiders (higher level) would replace them if I tried to go higher than 5 total. Needless to say, I put the interceptors back in.