It all has to do with FAR 117.

If the crew desk doesn't notify the crew of the delay until wake up time, they fear a fatigue call would occur later in the day due to the delay. The desk preempts this by waking the crew in the middle of the night and resetting their rest clock. They give the crew a new later report time which may mean that the plane sits for a few hours so the crew is available for a full duty period.