Since El Capitan it doesn't start properly

Since updating to El capitan have had a restart issue which was scary and it made me think that the hard drive was failing, Symptoms are on restart it would come up with no disc found, I then had to restart and use option and select the mac disc (the only option that is there) It then starts ok. The air is an early 2014 so just out of warrantee. I ran the start hold D key and the diagnostics say no problems found. The only way i have got it to start ok is select the start disc and restart. It then starts ok but makes me nervous as the apple logo comes up and the the progress bar runs (as if its loading an update) this happens every time - I think its a bug in El Capitan - anyone else getting this?

If so do i go back to before El Capitan or is apple going to fix this?