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!