I've seen this as well, but the main problem isn't that there's so many of them, it's that their transports don't take up any space population, so all eighty-some Barloz freighters start out on the map in addition to the defense fleet. For whatever reason, this makes the game lag terribly, to the point where it becomes nearly impossible to finish the battle. Assigning a population count to ground unit transports should help, although I haven't tried it myself.
This is also something I've only seen with the Rebels (multiple times) but never with the Empire, although that may just be me. I have noticed the Empire occasionally likes to spam TIE Fighters.