Yes. Occasionally some units bug out and become permanently visible. I've had this happen to me some weeks ago, and I don't know what exactly causes it.
There's 2 bugs with the IR HT.
One were you can make the beam stay on a single direction (although it's unreliable to put it on the direction you want) and the other is the one you describe.
Permanent spots happens when suppression is involved while the beam is on top of the units. I'm not sure if you just need the beam to pass when enemy units are affected by suppression or retreat while suppressed/beamed.