Airlines are known to run flights regardless of passengers just to hold down a regular route schedule and landing gate — what the industry called “keeping slots warm” — so that even an empty jet takes off on time. For example, it was recently reported that Lufthansa Group, which owns the German airline by the same name as well as Austrian Airlines, Swiss and Brussels Airlines, “will have to carry out 18,000 extra, unnecessary flights just to secure our take-off and landing rights,” their CEO Carsten Spohr said.

This is the root cause of the empty flights. I don't know enough about how airports and commercial air travel to understand why you have to 'keep the slots warm', but there probably is a reason for it other than just incompetence.

I'm guessing there is a lot of bureaucracy in airports with lots and lots of rules that have to be followed. Bureaucracies frequently lead to inefficiency and pointless results when rules still have to be followed when it doesn't make any sense.