My two posts (the one about interceptor bug and
the one about odd interaction of vanilla executable with X:CE mod) are also meant here.
Wrt. LOS issues: personally, the thing I've noticed is that on some maps with thick tree groups some of the tiles aren't getting uncovered from black state, regardless of how much you walk around them. I think I've occasionally seen that happen with water too.
Oh, I've recalled another thing, though this one might have been on purpose: on some of the larger UFOs you can see into the UFO from the outside, even though there doesn't seem to be any obvious LOS toward that place (often happens with a Xenonaut on the ground floor and an alien on one of the higher levels).
...and one more thing, though I'm not sure if I've really seen that or am just misremembering things: when the first cruiser with a valid leader (that is Caesan, as Sebillians don't carry Battle Rifles), I went immediately for a mass capture (fetched most of the bridge crew); the thing is that it's also the first ship to carry wraiths, so I got one of those (probably more) too.
Now the part I just might be misremembering: the bridge was obviously the last place to clean, so the mission ended with the last capture; as the summary appeared, I'm all but certain, that while the wraith was listed as taken alive, CL was listed as executed, even though it was the first leader alive *and* later the Leader research item was also unlocked. As it was the first cruiser raided, quite a few ship items were listed as sent to research, so I wonder if some limit wasn't mistakenly triggered for the list...
Obviously, the above is close to impossible to prove without a save....