I've noticed sometimes that regular enemy Aleph signatures just disappear when they go into cover or behind a wall. I know they're there, since I can hear them, see their shadow, or see them on the radar, but I don't see their red glow through cover.
When they pop out of cover to take a shot and then return to it, their Aleph signature does come back though.
So far, I've only seen this happen with Hades troopers, so I'm not sure if this is a bug that affects those enemies or if it also occurs with the 5th Council and Wardog enemies.