Was this yesterday/ today (18th) by any chance?
I checked in for the 1:45am flight from HKG to DOH and we boarded even though people checked in for the flight before had not taken off... On my flight it was only at around 90% load (that is what the check in staff informed me).
I have not looked into the details for the EU guidelines, but i thought it was for only flights starting in the EU...