Yea, I think that if there are above a certain number of other mobile military (non-carrier) AI enemy units on that planet, the carriers are invincible. This is to prevent a ton of ships being ejected and the game slowing to a crawl. Thankfully, the cap is pretty high, like 2000 or something, and the carriers are probably not as threatening as those 2000 ships, so you probably aren't missing much but not being able to take the carriers out right away.