Uefa has opened disciplinary proceedings against Atletico Madrid and Bolton following crowd trouble during their Uefa Cup tie on 21 February.
Bolton supporters were baton charged by Spanish police in Madrid
Fighting broke out outside Atletico's Vicente Calderon stadium after Bolton's 1-0 aggregate win over the Spaniards.
Bolton said supporters were subjected to "over-zealous and disproportionate" policing throughout the match.
Reports have been sent to the Uefa Control and Disciplinary Body, who will make a decision on Thursday, 20 March.
Spanish police said the problems, which saw 17 away supporters injured, were "just the usual at any football game" and refused to respond to Bolton's allegations.
Greater Manchester Police (GMP), whose Chief Superintendent David Lea was in the Vicente Calderon stadium, insists Bolton fans were not at fault and has pledged to help the club compile a report to Uefa.
Unfortunately the Madrid police have a reputation for not taking dissent very well
Chief Superintendent David Lea, Greater Manchester Police
BBC Sport's Ian Brown, who was commentating at the match, told BBC Radio 5 Live: "I saw three little pockets of trouble. But I did not see anything as serious as has been described.
"The first trouble I saw was from the Atletico end involving supporters from within that club.
"Then I saw a minor problem with Bolton supporters and the police were involved.
"At the end there was another incident with Bolton fans, some seats were displaced there and there was police involvement.
"I'm not sure who was responsible for throwing the seats around but the police do tend to respond quite quickly when something like that happens at a Spanish football ground."
I have great sympathy for any of our supporters who have been injured by what is clearly an overreaction by the Spanish police
Bolton chairman Phil Gartside
James Kirk, one of an estimated 3,500 Bolton fans in Madrid, said: "We came out of the stadium and just as we came down loads of police with shields and batons rushed back just where we'd come from.
"They were battering people to the ground - it was absolutely brutal and appalling. I've been to Spain many, many times but I tell you I don't want to go again."
Bolton chairman Phil Gartside added: "I have great sympathy for any of our supporters who have been injured by what is clearly an overreaction by the Spanish police.
"Bolton Wanderers Football Club will be pursuing the matter at the highest level and seeking an explanation from the Spanish authorities."
Ch Supt Lea said the problems started when police baton-charged hundreds of Madrid fans out of the stadium.
"That incident has probably set the tone for the policing of the whole match and unfortunately the Madrid police have a reputation for not taking dissent very well," he said.
The police chief said a number of sporadic incidents followed which resulted in police being "very heavy-handed" with the Bolton fans, and he blamed senior officers for the problems.
"They didn't have enough control over their junior officers who were far too quick to use their batons rather than talking to the fans who would comply with their instructions.
"Lessons need to be learned and I will make sure that my observations will be captured in a full report for the Uefa security investigation that I know is going to be forthcoming," he added.
It's not the first time British fans have been caught up in violence in Spain.
In a similar incident last November, following Aberdeen's Uefa Cup tie with Atletico, several Dons fans were injured in violent clashes with police.
And last April, a number of Tottenham fans were injured at their Uefa Cup tie in Seville in clashes with Spanish riot police.