This is a pretty minor bug, but I did just lose a promising run to it so I'm gonna report it as a way of venting. I had an OMNI Hunter in the DLC mid-climax who kept noticing one of my agents who was behind cover or walls and should have been undetectable (the guard would get suspicious, not alerted).

I have frustratingly little info about what caused this bug (I rarely even make it to Day 4), but I suspect it may have something to do with the guard's Ultraviolet Scanner. The text of the ability says it detects agents who are cloaked or disguised, and while my agent was neither, they did have a Subdermal Cloak augment installed. I know it wasn't the guard's Long-Range Scanner, because this was happening during the guard's turn, and the Long-Range Scanner triggered separately at the start of my turns.

If I get any more info on this bug I will update this post, but for now this is all the info I have.