Wolves submitted a formal complaint to UEFA after receiving "an unprecedented number of complaints from supporters who were left disappointed, distressed and in some cases injured" while entering the Braga Municipal Stadium.
The match finished 3-3 but many supporters only saw the last two Braga goals after being held by police and security guards on a field outside the stadium.
Police, who were wearing body armour and helmets, were criticised by supporters for using batons on Wolves supporters, with claims women and elderly people were injured.
Meanwhile footage showed a chaotic situation at the turnstiles as all the Wolves fans were funnelled through just one block.
Wolves thanked supporters for sharing their experiences and said it was waiting for a response from UEFA, while Braga emphasised that all the issues were reported outside their stadium and that Wolves did not apportion blame to Braga.
A statement released on the Braga club website said: "In the statement released by the English club, at no time are responsibilities attributed to SC Braga for the facts reported to Wolves by their supporters.
"It is important to highlight the absence of occurrences within the Municipal Stadium and that throughout the match a healthy environment prevailed, allowing fans of both teams to enjoy the game and their emotions.
"Also SC Braga takes the safety of the fans extremely seriously.
"In this sense, even though it has not been notified by UEFA or even targeted by Wolves, it will follow the reports of all parties involved with interest, seeking to confirm any excesses committed by some supporters, as well as the procedures adopted by the forces, police and security.
"SC Braga has extensive and successful experience with UEFA in organising games for European competition, gained over consecutive seasons in major events and against opponents from various countries, whose supporters have been welcomed by the club and the city."
WATCH: Police break up violence in Porto
Meanwhile a spokesman for Portugese Public Security Police, who were dealing with fans outside the stadium, told the Express & Star: "Regarding this game, we have no such reports and/or reports of serious events.
"Delays entering the premises and/or a large amount of supporters arriving last minute at the same time, usually, have a serious impact on the time people need to go through security checks, which will be, at all times, thoroughly performed."
Fans had flags, food, bags and electrical equipment confiscated despite the Foreign Office and Wolves not listing any of these items as being prohibited in the stadium.
The match happened after two nights of violence 30 miles away in Porto as British fans were targeted by hooligans believed to be supporters of Belgian Club Standard Liege, who were playing in a different nearby town in the same competition on the same night.
Several people involved in the violence needed hospital treatment and one British person was arrested, but Portugese police have not confirmed what action was taken against the suspect, if any.
The police spokesman did however confirm that rubber bullets were fired three times to break up disorder in Porto.
Around 6,000 Wolves fans are thought to have travelled to Portugal for what was the final away match of the group stages.
Wolves, who have already qualified for the knockout rounds, will play Besiktas at home in their final group match next Thursday.