I think you’ve got an issue with Mutogs causing game freezes. I noticed this once I started doing missions against Anu… either raids against their structures or defenses of Jericho Havens against Anu attacks. I’ve had multiple times where the mission freezes on the loading screen when particpating in a raid against Anu (energy sector) or defending a Jericho haven against Anu assault. At first I had no clue what was causing this. The freeze seemed to happen consistently on one Anu haven but I did a raid against another Anu haven and everything worked just fine. Then I tried to do a defense of a Jericho haven against an Anu assault and the same freeze on the loading screen would happen. However, I reloaded from a save and was able to run the defense mission just fine (No Mutogs were among Anu forces).
I got another Haven defence against Anu and the game loaded and I was able to play the first turn or two of the tactical battle but I noticed as soon as a Mutog showed up as a reinforcement for Anu, the game froze on the enemy turn…I could f12 to do the report but the enemy would never complete their turn. I reloaded from a save on the Geoscape layer and let the game run for a little bit and Anu attacked the same Jericho haven again. This time I got a different map and I saved at the beggining of the tactical battle… played through the first turn, killed a couple of Anu troopers but on the 2nd turn when a Mutog showed up as an Anu reinforcement, the game froze as before. I loaded the save I made from the start of the tactical battle and this time was able to kill all Anu forces on the map on turn one… the mission completed successfully without freezing.
I have been able to do complete multi-turn missions against Anu but only when no Mutogs were present in the battle… at this point, it seems fairly consistent that something is bugged with them.