United edged past West Ham at the London Stadium following second-half goals from Juan Mata and Zlatan Ibrahimovic.
The Hammers had battled admirably after Feghouli was given his marching orders after just ten minutes for a lunge on Jones.
It looked like a harsh decision from referee Mike Dean - but Mourinho claims he missed the incident.
"Job done, but congratulations to everyone on the pitch because I thought it was very hard," Mourinho said.
"I was disappointed by some mistakes and decisions on the pitch, but that is fatigue, there are no miracles.
"We kept a clean sheet because David De Gea made a good save from Antonio, we had to move the ball and create space.
"I had Mata and Rashford on the bench to bring a different intensity.
"I didn't make anything of the red card. I was too far away and did not watch it on television.
"I have had to educate myself in the first half of the season because of so many decisions - Zlatan's disallowed goal, a clear penalty against Crystal Palace.
"It is great for the fans and the people at home, but it is hard for us, even for me."
