If your enemies are geth then some of them can "see" through the cloak. For example through Javelin sniper rifle scope and such.
I'd say I did have the same problem but I never considered that a bug as I think enemies just continue to shoot at the same general spot on automatic for a couple of seconds, that's why I always change positions the second I activate the cloak.
In one thing I think you are right - I don't remember it being that way in original as I always used cloak to escape when being cornered.
