Shaw addressed this situation play #3 of the training video this week. Basically said the crew was wrong to not enforce the penalty without saying they were wrong, and that adding one or two seconds back would have to be an on-field decision and could not come from replay since there were less than 3 seconds and the clock would start on the ready.
Yeah, my takeaway was that they should have either A) put :01 back on the clock, moved the ball forward 15 yards, and then see if the offense could snap the ball before time expired -- or -- B) declare the half over and enforce on the second half kickoff.
What they did instead was to put :01 back on the clock, move the ball 15 yards, then state the offense couldn't possibly get the snap off and the half is over... but then not actually doing those first two things since they declared it moot.
What I didn't like about the video is that it seems like the crew had a choice here. By refusing to say the crew did it wrong, he couldn't clearly state what they should have done. I think the correct call would have been to allow the offense a chance at an additional play with :01 left, but that would have been nice to be more clearly stated.