The cap is a leftover from the systems where scientists / engineers were gained on the Geoscape. Looks like I set the cap at 50, which probably is a bit small. I'll increase it to 250.
Ugh. That's a bug too - the mission isn't meant to end if you kill all the enemies. You need to pick up the items and take them back to the dropship, and enemy reinforcements will keep spawning until you do. We'll have a look at that too.