With Pompey leading 1-0, Mowatt struck the post from 12 yards before slapping Thompson after the defender had run a number of yards to celebrate the failed spot kick in front of him.
Mowatt was subsequently sent off, but Robinson has questioned why Thompson did not receive a second yellow card for what he describes as 'unacceptable' behaviour.
The 37-year-old told BBC Radio Oxford: "He's run fully 20 yards to stand in Alex's face and goad him. I've not seen that for a long, long time. That's a booking, he was booked in the first half too.
"What Nathan did today wasn't acceptable on a football pitch. If one of my players did that, I'd tell them the same and reprimand them accordingly."
Portsmouth went on to claim a 3-0 victory at Fratton Park.