I was playing a nice long 3-way slugging match with the AI on Normal (yeah, yeah, I'm still learning), preparing to finish off the pirates after taking out the two AI players (game was already won, but I don't quit until everything's MINE). A max-rating pirate fleet was sent after me as my bounty was over 3,000. I arrived in the pirate system just as the pirate fleet was launched, and the enemy ship arc was completely full. I thought "Ooh, this should be fun" and tried to pick off as many ships as I could before they fled for their target. Here's where it gets wierd.

I had a pretty good force for the job but by no means overwhelming: a Kol (lv 4), Akkan (lv 8), Dunov (lv 4) and Marza (lv 6) plus 8 or so Kodiaks, Hoshikos, Gardas, and Javelises each (about 40% of the friendly ship arc around the planet was full). I had researched roughly two-thirds of the  military tree. However, by the time the pirates got out of the system, a matter of only 15-20 seconds, nearly two-thirds of their ships were destroyed and every capital ship leveled up in the process. The damage they dealt seemed normal though, as several ships took enough damage that they would have gone poof if I didn't have the Hoshikos and Dunov on hand. The pirates continued towards a poorly defended colony as I tried to chase after them. The colony was guarded by only two Guass platforms and a Hanger with 1 Bomber and Fighter each. Even so, in the short window between the arrival of the strangely-tiny pirate fleet and my own pursuing fleet, another 15-20 seconds time window, the remaining pirates were wiped out almost entirely by the two strikecraft squadrons, with the Gauss platforms and pursuing ships barely getting in any shots.

The pirates had normal strength throughout the entire previous game, it was only this single encounter that they were so weak. Upon returning to finish off the pirate base itself, their Gauss platforms and the base itself had normal durability. I've got a replay available, but the quirk doesn't occur until around 3:25, so I'm not sure if anyone would even want to sit through the game long enough to see it occur.

Edit: Nevermind, I was underestimating the power of the Marza'a Missile Barrage. The entire pirate fleet (of weak, fragile ships) had bunched up just before a combined launch of Missile Barrage and Radiation Bomb. There wasn't much left for the rest of the fleets to deal with after that much doombringing.