The 3 groups that spawn, are all the same quality. If you battle 2 and mark one with a raid symbol but leave it up, they will automatically respawn as that particular pet. So when you come back to that group, the two unmarked ones will be new quality/combo of added pets, but the same primary pet type. You have to mark one, so you know which one is the remnant of the old group. This makes farming for a rare easier. I've heard it used mostly on the gilded moth 3 groups (so they will spawn as battle pets instead of critters each time, but you will automatically get a new quality).
Edit: did I explain that well?
Also, I think in my initial post my observations were just glitches related to the server restarts. After about 20 mins it stopped happening.