When primes start showing up on haven defense missions, the aliens start killing way more civis each turn, making these missions WAY harder. If you want to see this in action you can see Llamachomp's stream from 9/20 or Lollash's from 9/21. They are playing on legend with ABC+, 8 man squads, and ABM, but I've seen this in my game on commabder without those mods as well. I had the aliens kill 4 civis in one turn.