Whats wrong with the hybrid system?
But one thing is that the parts of the hybrid system are different than normal gas cars. The transmission is probably different, and the gas engines are smaller. So most independent shops don't really have experience working on those hybrid-specific parts.
Another thing is that the HV batteries don't last forever, and are expensive to replace. And the warranties don't always cover the average life of a battery.
The third thing is that hybrid battery is high voltage. So most shops won't want to do any repairs that will touch the HV electrical system.
You can find independent mechanics that work on hybrids, hybrid car repair just require a little more specialization than other cars.