Okay, so I'm sure that I'm right about this now.
What really confuses me is why nobody discovered or reported this huge issue previously though ?! Is it so hard to arrange situations where you should see units ?
Fixing this bug will greatly reduce difficulty in 2.5 again, which everyone complains about, as these IR goggles are the main way of knowing that an enemy is about to ambush you, so that you can kill it before it's got a chance to kill you, or flee, or prepare for the ambush.
Attached is a save with one of the harvester missions - as it's not possible to save during missions, a more deterministic way of reproduction is not possible. On this particular map, in 2.4, it was so that most or all of the enemies stayed in the UFO, and one could look into it with IR goggles to detect positions, weapons, their number and so on, before luring them out one-by-one or in small groups. It does no longer work that well, but I very likely should have seen that one Taman that was still in the UFO.