Modern planes have comprehensive sensor systems for all door operations. If a door is not fully closed it's presented very obnoxiously on the flight deck, so I'd bet something either broke in flight or a sensor system was very out-of-tolerance.

Going beyond that, I thought modern planes were designed with plug doors and latches that physically can't get partially engaged.

If you're depending on a sensor alarming on the flight deck, you're already several failures in I would think.

Thats for passenger planes. Cargo aircraft don't want to sacrifice the swing in area.