The Red Devils arrived at Old Trafford only 45 minutes prior to kick off of their encounter against the Spanish side, forcing them to delay the start of the match by five minutes as a consequence.
United were poor during the encounter, eking out a 0-0 draw against the Spanish club, earning them their fourth point from two games in Europe, following a 3-0 opening-game win over Young Boys.
Mourinho blamed the delay on Greater Manchester Police, insisting that they refused the club's request for an escort to the stadium, leaving the Portuguese and his players in traffic for over an hour.
"We left the hotel at 6 p.m. hoping that 30 minutes would be enough," said Mourinho. "It usually is. But this time the police refused to do an escort, so we came by ourselves.
"From the Lowry Hotel we took 75 minutes. UEFA and the referee were nice to allow the match to start five minutes late.
"It was not a problem with club organisation. We were informed that the police refused an escort."
Chief Inspector Andy Sutcliffe, GMP’s Silver Commander for the fixture, indicated that Mourinho’s version of events is not strictly true.
In a statement, he said: “All police deployments are carried out following a comprehensive risk assessment process and, specifically in respect of escort team buses, are only ever undertaken on occasions when there is intelligence or information to suggest a risk of threat or harm to the players.
“GMP has previously used police vehicles to accompany a team’s coach but after a review of our core policing responsibilities, it was decided that we would no longer provide this service at every fixture.
“We consulted with the relevant football clubs over a period of months to allow them adequate time to plan ahead for their journeys to the stadium."
Valencia have also been charged with a kit infringement, and for supporters letting off fireworks.