"Inexperience." SpaceX is now up to 100 launches, two of which had catastrophic failures. The flight that destroyed a Dragon on the way to the ISS was survivable if the capsule was manned and had an active launch escape system (Launch Escape was not an option on the cargo flights). The one accident on the ground was not related to the fueling itself but instead a flaw in a Helium tank that ignited crystalized oxygen. THAT accident would have happened no matter how the rocket was fueled. SpaceX has been working on the Load-And-Go for some 40 launches now over the past five years.
NASA already signed off on this way of fueling the rocket as the technology and procedure is well understood. SpaceX is not the only company loading supercooled propellants into rockets either; the French do so with Ariane. NASA did not do this with the Space Shuttle due to the crew sitting on the side of the fuel tanks and no way to bail out quickly and safely on the ground in the event of a fueling mishap. Putting the astronauts in the capsule, and getting the ground teams away from the rocket while fueling has safety benefits.
Shit like this is why we are still relying on the Russians to get people into space.