I've seen quite a few instances where the AI would seemingly spot and attack me through walls and ceilings. I think it may have to do with the prediction and the fact that the AI knows exactly if you're still a viable target. Also some objects seem to be partially see through for the AI, namely window shutters and closed doors. More than once I was shot through closed shutters, after the AI became aware of my position in that building.

Hey and thank you for the report!

The AI can also hear you, currently it can hear you sometimes too well (because of this bug: http://feedback.arma3.com/view.php?id=23345)

If the AI thinks the bullets will penetrate it may decide to shoot even if it only has an estimation of the target's position based on the target's noise. (but it needs to know first that the target is an enemy - which shouldn't happen because of the footsteps only. Audible fire or visual confirmation is required.)

Could this be the cause?

Perhaps, yes - the enemy doesn't always hit (but they are directly above me with a machine gun, so it's not too hard).

Because I can't see them, I don't know whether they've spotted me already or not.

I'm fairly certain they haven't seen me directly (they're inside the room, I'm below and I entered out-of-sight of the window) - however, I've been in a firefight with some of their friends, so they may be on alert.