This happens all the time to me, regardless of whether I leave the overseer window open or not. And regardless of whether I just logged in or not. It happens so often I've gotten in the habit of checking my Agents list before starting more quests. The timer shows (0h 0m 0s) and the agent is still incapacitated. As I scroll through the agent list they will all of a sudden clear the incapacitation. Sometimes I have to click on them to get it to do it.