@Sphere: I think Decker says something about a faulty backup crystal in the transporter circuit right before Kirk comes to relieve him. Seems like that might be a part of a failsafe system.
I know we're getting more OT, but...
That seems like it makes the transporter malfunction even more negligent, either with something in the initial design allowing transporters to work without a failsafe, or with the engineering staff who allowed it to do so. It seems to me without the failsafe working the transporter system should have been automatically taken offline. After all, it seems it was offline for the majority of the time the Enterprise was in the dock. So what's two more crew members being brought up via shuttle? Of course plot wise then you wouldn't lose Cmdr. Sonak thereby making room for Spock to come back.