Steven Bergwijn gave the hosts a 1-0 lead in the primary half, after David De Gea neglected to keep out his ground-breaking shot.
Nonetheless, United leveled from the spot through Bruno Fernandes, after Paul Pogba was fouled in the territory by Eric Dier.
Ref Jon Moss granted the Red Devils a penalty, however VAR overruled the call.
“I am unhappy with the VAR, not the referee on the first, the referee can make a mistake but VAR is there to do the job.
“In the second I am unhappy with Jon Moss because he did not give the free kick leading up to it and then gave a penalty. In this case, the VAR gave the truth,” Mourinho told Sky Sports.