I have found that it can be easy to trap all the aliens in the UFO if you are on a map with a landed Harvester. Run one man up to the front of the Harvester, right next to the front chambers. The aliens all can see you somehow and will try to get you, but they can't figure out that they have to leave the UFO first. They all congregate in the forward compartments, right next to your man. Clear the area, then move the rest of your team around the back and set up a kill zone. Then move the man up front away from the UFO and the aliens will head toward the rest of your men out back. You can sometimes regulate how many aliens will leave by how far away you move and by moving back after a turn.
It's cheesy, but I look forward to the day that it doesn't work because the AI can pathfind out of areas with limited access.