I have had this happen before. As others have pointed out of the FAs need to be on board for the the plane to though the captain or co pilot approves boarding. As others have said anyone of a number of issues might have occurred. Most likely is a pilot that called in sick at the last minute or was pulled at the last minute for another flight or overslept
Flight can board because FAs are on board for safety purposes and copilot sees no reason for a delay pilot is assumed to be on his way because nothing is known that would cause one to believe otherwise.

Last it happened to me the pilot had set his alarm and his iPhone hadn’t adjusted to the correct time zone. I know this because I overheard it. Oddly enough he didn’t even recognize he was off by an hour until he got to the gate. We were only delayed about thirty minutes because we were loaded and ready to go the copilot had done all the checks and the pilot was about what he thought was forty minutes early for the flight so only really 20 minutes late