There was unrest as Rangers fans attempted to enter the stadium before kick-off, while reports suggested some away supporters ripped up seats during the match.
Bain claimed a promise that four turnstiles would be open for visiting fans was not kept, causing problems which were compounded, he claimed, by police using CS gas against angered Light Blues' supporters.
Bain said on Rangers' official website: "Obviously the behaviour of some of the fans inside the stadium was unacceptable and no-one likes to see that.
"However, what was equally unacceptable was the fact that Rangers came to this stadium with representatives from UEFA and Unirea a number of weeks ago and arranged for the four turnstiles to be open to give access to our supporters.
"When they arrived this evening, there were only two turnstiles open which caused difficulty gaining access and fans then to be sprayed with CS gas is totally unacceptable.
"I will now make representation to UEFA in their behalf."
Trouble at the match was described as a "minor incident" by Andy Kerr, president of the Rangers Supporters Assembly.
Kerr told Sky Sports News: "There was a bit of pressure at the front. Spray was used, which was used before the start of the match, and I think people reacted to that.
"I wouldn't say the Rangers fans did anything wrong. The organisation was very poor.
"(Before the match) they had two cordons of barriers to let people through. They used the spray there on more than one occasion and people were quite distressed by that."
Kerr did not see any fans ripping up seats, but stressed such behaviour was unacceptable.
"We don't condone it, we don't want to see it, but the vast majority of people behaved impeccably," he said.
"In the big scheme of things, (it's) a minor incident."
Kerr recalled a similar incident at an away game in 2005.
"The last incident I could remember was in Bratislava when we played Artmedia," he said.
"They almost seem surprised that we all turn up about a half hour before the game."