Therein lies the likely explanation. If you had simply shown the boarding pass minus certificate, nothing would have happened. Since he saw the certificate, he would have assumed that the GA had mistakenly neglected to collect the cert, so he thought he was doing the GA a favour.

While you were delayed for several hours due to previous flight cancelation, the flight in question's delay was only 45 minutes. Given the relatively short delay, I would not have expected free food/drink.