I have only had this happen once so it may be a fluke but I was playing as TEC Loyalist when a Ragnarok and small attendant fleet  attacked two of my starbases in the grav well of a Gas giant (had twin fortress research).  I had the the starbases close enough to where people could jump from one to the other if needed so they were both tearing the Ragnarok a new one with the Rag (heh) focusing on one starbase.  The Ragnarok was using the special weapon whose blast repulses nearby ships.  One of the shots however, repelled the sister station and it didn't stop until it was nearly out of the grav well.  This sucked bigtime because I no longer had the combined firepower of both and the Rag wasn't alone.  I have the save game if needed.  Just wanted to mention it and make sure this is not "expected" game behavior.