hi, it happened to me once. thought i get free pass :P but then realised they have it all in their system.
when i went back to the airport for my flight out, at the exit immigration, they checked and asked me to go into their office to settle the outstanding QR100.
so if you don't want the hassle and wait time when exiting the country, i would advise to go get it sorted out beforehand. also be mindful of the 30-days stay - they charge QR500 for each day of over-stay. one of my colleague over-stayed 7-days = QR3,500 had to pay before they let her exit the country. cheers :)