This sounds like something I just had happen to me, except *way* earlier in the game. Probably only a couple of hours in with three planets captured and an AIP of only 57. I had eliminated the final jump gate leading to my homeworld, and had one other planet with plenty of jump gates around it. I was in the middle of an assault against a juicy AI planet, not too tough, but it had some nice capturables and resources, when a 620 Bomber MkII wave targeted my homework. This was not a CPA or ?? type wave, it was an actual count-down based, single planet attack---but it came out of the middle of space instead of any wormholes. Being that early in the game, I didn't really have anything that could counter it, especially with the 3 minutes of warning it gave me. I wasted a bunch of knowledge teching up to MkIII fighters and tried to pump them out as fast as possible but could get nowhere near enough to stand up to the wave in the time it took for it arrive, even pulling all of my riot ships in to help. The wave also had a fairly strong mix of bombards and fighters. Given that the game was only two hours in, and even adjacent planets were still sitting at about 160 units total, border aggression or scrap fleets really shouldn't have been in play. According to that galaxy stats, there were only 7,000 enemy units total, meaning this wave represented nearly 10% of their entire fleet.
It was kind of frustrating since it came so early and I don't think I could have fended it off even if I knew it was coming from the very start of the game and had been preparing for it all along.
Any idea what could cause that; how to avoid it in the future?