Actually, I forgot to report this one, and I guess it might be ubiquitous, but I found that such lock-up happens to me a lot with small UFO with Vipers or Gorgols inside - they get "reaction shot" from a distance, and AI can't seem to decide what to do.
Simple "fix" I found is a) save before entering small UFOs b) liberal use of explosives to make sure one shot = one kill c) super-buff reaction-proof peoples d) first go point-blank to viper then fire, it will retaliate (bite you) on reaction instead of locking the game up.