Ah--I didn't know about the rebels as I have played Advent and Vasari mostly. That would be the attack out of nowhere but it fits quite well with my map design intent--very cool and thanks for the info. It's a small force compared to a pirate raid.
The pirates came on a different map and definitely moved from at least one planet to two others off of phaselanes/wormholes. In one case, I was able to move my ships halfway to another planet while pursuing them.
So it looks like the rebels explain my recent incursion--the pirate raid came before the latest update so perhaps that has been corrected. So I gues now I just want the rebels and I want them alive commander!