It is understood Mourinho confronted Clattenburg in the tunnel at half-time after United were denied a penalty following Jon Flanagan's apparent trip on Matteo Darmian in the first half.
Former Man United defender Paul Parker questions whether Jose Mourinho's behaviour is distracting the squad.
The United boss said it would be "difficult" for Taylor to officiate their game with Liverpool prior to the match at Anfield on 17 October.
Manchester United manager, Jose Mourinho, has been handed a one-game touchline ban and fined £50,000 by the Football Association, for two separate incidents involving referees.
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He was also fined £50,000 for saying that referees were afraid to award penalties against his side after the Blues were beaten 3-1 by Southampton in October 2015.
Separately, Mourinho was handed a 50,000-pound ($61,000) fine for comments he made about referee Anthony Taylor before United's game at Liverpool on October 17.
"The commission found the disrepute element of the charge proven and as well as being fined, Mr Mourinho was warned as to his future conduct".
Mourinho conceded he may have to include Jones, who has been named in the squad to face Fenerbahce after recovering from a knee ligament injury, in Thursday's Europa League clash due to the absences of Antonio Valencia, Eric Bailly and Chris Smalling.
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Under FA rules, managers are banned from commenting on match officials before matches.
The Atletico Madrid centre back is one of the most highly-rated young defenders in the world and Mourinho is prepared to put up more than £50m to secure his signature ahead of interest from a host of other top European clubs, according to the Mirror.
"But of course we get to do what he wants doing the whole week so we've got him for the whole week, so there's no sort of worries if he's not going to be there".
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