I'm not sure how much that can be helped. Sometimes the random spawn creates more of those units than at other times. If you're unlucky, it can make for a long fight. Unfortunately you don't have much control over that, other than to try not to have more than one squad in the fight at a time.
Bingo. Also, some of these were high rank NPCs, which compounded the issue I mentioned previously. I've spent quite a bit of time with the Foundry going back to closed beta, so I know you can make balanced missions