Television pictures showed a number of Rangers fans clashing with Romanian police in the stands at half-time, while one supporter was seen to rip out a seat.
Chief executive Martin Bain has condemned those involved in the violence but blamed poor organisation and over-zealous policing for sparking the trouble.
Superintendent Mike Dean of Strathclyde Police, who was helping to co-ordinate security at the Steaua Stadium, agreed.
He said in the Daily Record: "The situation arose because, despite having an agreement in place with UEFA that four turnstiles would be in operation, there were in fact only two.
"I was there with the UEFA delegate from right up until about 20 minutes before kick-off time, when there was a late surge with 400 or 500 supporters trying to get in through two gates.
"At that stage, the public order riot police went in and sprayed the fans. This caused a lot of tension and the whole thing deteriorated. Fans were still trying to get into the ground at half-time.
"What happened inside the stadium at half-time was probably a direct result of the tensions outside. I was not happy."
The matter will be dealt with by UEFA's control and disciplinary body on Thursday.
Dean, who has has already spoken to UEFA to give them his on-the-spot version, added: "Eventually, we went to the control room and spoke to the match commander. He got very excited and started shouting when all I was attempting to do was give him my advice, with 10 years' experience of these kind of things.
"He then decided he needed the stewards to remove some of the Rangers flags, to clear seats for the fans who were still coming in.
"I told him the fans will do that themselves. But he chose not to take my advice. It was at that point a steward went in to remove some flags and was challenged by the supporters. I can't condone those fans who came rushing down from the back and would warn them the CCTV pictures are of tremendous quality."
Responding to Thursday's charge, Rangers chief Bain said: "We have been informed by UEFA that disciplinary proceedings have been instigated in relation to the throwing of missiles and crowd disturbances.
"As already stated, I am not for a moment condoning the action of some supporters to the unfolding of events within the stadium.
"But, as a club, the preparations which were agreed and insisted upon in advance were not adhered to and this in turn we feel jeopardised the safety of our supporters.
"We are fully aware of the indiscriminate use of CS gas and the difficulties experienced by our fans accessing the stadium.
"All these factors will be presented fully by the club to UEFA in our submission."
Wednesday night's trouble was the latest instance of Rangers fans landing the club in hot water with UEFA.
The Light Blues were fined £13,300 for supporters' discriminatory chanting and £9,000 for attacking their opponents' team bus during an away game against Villarreal in 2006.
The following year, they were fined £8,280 on an improper conduct charge for fans' behaviour at an away UEFA Cup game against Osasuna.
Supporters have also been in trouble with police, with the rioting during last year's UEFA Cup final in Manchester regarded as one of the most shameful episodes in the club's recent history.