Stewart Regan, the chief executive of the Scottish Football Association, has defended referee Craig Thomson for his performance during Malaga's controversial exit from the Champions League quarter-finals in Dortmund.

The Spanish club conceded twice in stoppage time on Tuesday to lose the tie on aggregate.

Both of those goals appeared to be offside and Malaga have made an official complaint to UEFA over Thomson's failure to disallow them. Indeed, the club were so disillusioned with their exit that president, Abdullah Bin Nasser Al Thani, later accused European football's governing body of being "corrupt and based on racism".

Regan was more relaxed with his comments, although they were also contentious since he laid the blame for any mistakes at the feet of Thomson's assistants, Derek Rose and Alasdair Ross.

"Craig Thomson has had a fantastic season and that was why he was selected to referee a Champions League match at the highest level. I thought his handling of the game was very, very good," said Regan, who hoped the controversy would not affect Thomson's selection for the World Cup in Rio.

"Unfortunately a number of decisions for the people working alongside him perhaps let him down. But these things happen. It doesn't get away from the fact that Craig Thomson is a first-class referee and that's why he has risen through the game in the way he has."

Thomson was not the first Scottish official to incur the wrath of a European club, with Willie Collum was criticised by officials at Lazio following an erratic display in their Europa League defeat by Fenerbahce. However, such was the ferocity of Al Thani's comments, UEFA are to examine if there are grounds to take disciplinary action against the Malaga president.

"Yes, we were targeted from the beginning of the season by corrupt UEFA and based on racism," he posted on Twitter. That follows similar sentiments in comments made in December, when Malaga accused UEFA of unfair and unjust treatment after they were given a one-season ban from European competition – to be imposed if the club qualify for the Champions League or Europa League during any of the next four seasons – due to outstanding debts.

"It will now be analysed by our disciplinary inspectors," said UEFA general secretary Gianni Infantino. "When you lose a match in the 93rd minute, maybe you say things that you don't really think and you really don't want to say."