because the Enterprise transporters weren't operational yet -- the engineering crew was having problems getting them to work. When Kirk arrived in the engine room minutes before the accident, the engineers' chatter was about "faulty modules" in the transporter that kept its sensors from engaging. Cleary was in the process of putting a new backup sensor in the unit, per Scotty's order, when the transporter room started to engage the transport. Essentially, because they were rushing to do a job in 12 hours that should've been done over days or weeks, mistakes were made, and the accident resulted from that. Kirk's hubris, his zeal to use the crisis as an excuse to get his ship back, has resulted in an unready ship being pushed into service, and two people have died as a result. And Kirk has to live with the consequences of his actions.
Why is Kirk responsible here when the sequence of events in the movie points to a mistake on the crew? Yes, we hear some engineers saying something was wrong with the transporters. They should've then locked out the system so no one would use it and test it until corrected - like they did in "The Galileo Seven". Instead no one bothers to do this or inform the transporter room of the problem until the accident happens. Kirk didn't give any order to override safety protocols so this is a crew fault which goes to Shatnertage's comment of an inept Starfleet.