Smalling was photographed wearing a leg brace on Monday after suffering his third injury of the campaign. Jones has a toe problem. "They are long-term injuries," Mourinho said.
United will be without at least six first-team players for Saturday's Premier League game against West Bromwich Albion as Smalling and Jones join midfielder Paul Pogba on the treatment table while Mata begins his recovery from the operation.
Leading scorer Zlatan Ibrahimovic and midfielder Ander Herrera will also miss the match at Old Trafford as they serve the final game of their suspensions.
Mourinho, however, refused to dwell on his lengthy list of absentees.
"The important ones are the ones who are ready to play. That's the way we have to think, we cannot be here crying or speaking about the players that are not available to play," the Portuguese said.
Captain Wayne Rooney, who has missed United's last four games, has recovered from a knee injury.
Mourinho said he regretted his treatment of Bastian Schweinsteiger, who joined Major League Soccer's Chicago Fire this month, and has apologised to the German midfielder.
Schweinsteiger was made to train with the reserves by Mourinho earlier this season but the manager had a change of heart and brought the World Cup winner back into his squad in October.
"I regret it and it is no problem for me to admit it, because I have told him," Mourinho added.
"He's in the category of players that I feel sorry for something I did to him... the last thing I told him before he left - 'I was not right with you once. I have to be right to you now'."
(Reporting by Shravanth Vijayakumar in Bengaluru, editing by Ed Osmond and Ken Ferris)
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