Liverpool, who progressed to the quarter-finals 3-1 on aggregate after Philippe Coutinho cancelled out Anthony Martial's penalty opener to secure a 1-1 draw in the second leg, faced more charges.
They were listed as illicit chants, the setting off of fireworks, throwing of objects, crowd disturbances and a late kick-off.
The case will be heard by UEFA's control, ethics and disciplinary body on May 19.
A handful of Liverpool fans sitting in the top tier of the East Stand, among the home supporters, unfurled a banner in the dying minutes of the game, sparking clashes in which punches were thrown and a seat hurled.
Liverpool fans in the lower tier of the stand began chanting "Munich" in a reference to the 1958 air disaster that killed 23 people including eight Manchester United players as the 'Busby Babes' flew home from a European Cup tie in Belgrade.
Police and stewards were forced to form a human shield to separate the two sets of supporters and Greater Manchester Police confirmed making five arrests and said they were investigating a "handful of concerning incidents".
"The policing operation for the Manchester United v Liverpool match has now come to an end and towards the end of the game there were a handful of concerning incidents which are currently being investigated," Superintendent Jim Liggett, match commander for the tie, told British media.
"We have made a total of five arrests."
Fans also lit flares shortly after Coutinho equalised at the end of the first half.
In the first-leg at Anfield, Liverpool's 2-0 victory was marred by a section of United supporters chanting about the Hillsborough stadium disaster, when 96 Liverpool fans died following a crush of bodies at an FA Cup semi-final against Nottingham Forest in 1989.
United avoided a UEFA sanction as the match officials did not mention the incident in their match report.
(Reporting by Simon Jennings in Bengaluru/Alan Baldwin; Editing by John O'Brien)
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