City assistant Manuel Estiarte posted footage from the bus on social media and called the incident "unacceptable".
Liverpool fans had planned to gather along Anfield Road to greet the two teams but, following discussions with the police, the club re-routed the buses along Arkles Lane, which is a dual carriageway and much wider - although longer - than the usual route.
Pep Guardiola, meanwhile believes his team are capable of turning around the deficit and says he will convince his players they can fight back in the tie.
However, BBC Sport understands the police are unhappy at reports insinuating the route notification was partly to blame for what happened.
"United found their game, found their actions, they have spirit".
The case won't be heard by UEFA's disciplinary physique till Could 31 after the ultimate, which means any sanctions would apply exclusively subsequent season.
Following the final whistle, Guardiola talked about how one has to remain consistent when playing the top sides, as well as expressing concern that this defeat might affect their confidence going forward. "One year ago something happened in Dortmund".
"Of course we wanted to win today, I'm not going to deny that but we knew exactly we were going to play against, the second in the league".
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Now instead of a morale-boosting celebration, Pep Guardiola's side have been forced to wait to clinch their third title in seven seasons and can not be guaranteed the title even if they win at Tottenham Hotspur next Saturday.
Liverpool made life hell for Manchester City - and that was before the match had even started.
"He's so strong, he knows how we like him, he knows how we support him", Guardiola said.
United reduced City's lead only to 13 points. "We will convince ourselves that we can", he said.
However, Guardiola's players were keen to play down the incident.
Guardiola reacted by ringing the changes, bringing on Kevin De Bruyne for David Silva and Gabriel Jesus for Bernardo Silva in what was suddenly a stunned atmosphere at the Etihad Stadium.
"It was OK", the Belgian said.
City's dominance has been so overwhelming that many are already ranking them among the best teams in Premier League history, alongside the likes of Arsenal's "Invincibles", who won the 2003-04 title without losing a single match, and United's 1999 treble winners.
There is no dispute that Guardiola is one of, if not the, best manager in the world and has been for the last decade but there has been a trend where Guardiola gets his tactical decisions completely wrong in Europe and it backfires terribly in his face.