Mourinho was also left frustrated with Luke Shaw's latest setback, with the fullback being forced off in the early minutes.
''I think Shaw has to be a big injury to leave the pitch after 10 minutes," said Mourinho, who has been critical of the left-back on several occasions this season.
The Portuguese added on BT Sport: "I prefer not to speak about Phil Jones and Chris Smalling. I prefer to speak about (unused substitute) Juan Mata giving everything to be available. I am grateful for that."
Time is short for United to pick themselves up for the next challenge, the small matter of a Europa League semi-final against Celta Vigo on Thursday, and although Jones and Smalling are not expected back, midfield reinforcements are due.
"I don't think they (Jones and Smalling) will, that's my personal opinion, I don't think they will but I know that the players I choose they give everything," he said.
"It doesn't matter if I go with (Matteo) Darmian central defender, if I go with (Michael) Carrick or Axel (Tuanzebe), I trust the boys, the spirit is amazing, the group is phenomenal. Fellaini and (Paul) Pogba will be back for that game, so we have more options and we try with everything we have and we go again."