Tottenham reached the fourth round of the Carabao Cup courtesy of a bye following a mass coronavirus outbreak at previous opponents Leyton Orient.
The League Two side wanted the lucrative tie re-arranged, only for the EFL to eliminate them from the competition.
"I think (Orient) have to be very, very upset. I think they have to, I have total sympathy for them," Mourinho said.
"I don't think they did anything wrong - they were tested, I think they deserve to play against us, no doubt about it."