I'm not excusing what I see as Harbaugh's routinely weak management of TOs and game clock... but that said... these clock management gaffes by officials too are another example of why I think the league should have a three-man crew in the booth upstairs that works with the on-field crew in real-time. The on-field officials not only have the job of watching each play and 22 players for penalties, complete vs incomplete, down vs not, etc etc etc... but they have to re-position themselves before each snap, spot or help spot the ball, break up conflicts between players, and communicate with each other while players, coaches, and (in another world) thousands of screaming fans are yelling at or around them from kickoff to triple zeros.
Put three trained, knowledgeable officials in a quiet replay booth upstairs with a direct line to the head official... and give them the power to control their own replays from the broadcast truck feed, stop play at any time to clarify, correct, or in some cases make a call that is missed, etc.
And for the love of God, the challenge system needs to be unlimited challenges at ANY time of the game... you burn a TO or take a delay of game penalty if you lose the challenge.