Map bug, flanked through high cover.

[Thrair]

Long War 1.1 (Fresh start, experimental campaign).
No other mods.
PC.
Have save file.

Following screenshot. Shinobi took two shots through full cover by disoriented targets. The Officer landing a shot was just XCOM baby, but since the first one was a crit from the trooper, I was paying attention enough to notice the yellow cover icon before my Shinobi bit it. I confirmed the map bug by moving a ranger to the same tile, who I am pretty sure was wounded through the same spot a turn earlier (before I had pulled 'em back on account of nearly biting it).

Not sure how fixable map bugs like this are, but figured I'd toss it out.

[LordYanaek]

This is an old vanilla XCom2 bug and the biggest reason i never played Ironman

[sectoidfodder]

These cover issues seem to happen pretty frequently (once every few missions). The soldier will also fail to lean-out with the cover that isn't counting for him, which sometimes results in LOS problems. Other times, blowing away an enemy's cover with explosives will result in him standing in the open but still getting cover defense bonuses and not being flanked.

Saving + reloading the tactical game reliably fixes these problems.