The Scotsman, returning to his former club for the first time since joining the Trotters in January, could only watch on as the his side suffered a 1-0 defeat at Turf Moor courtesy of Elliot.
"I spoke to him (Clattenburg) at half-time because I wanted to be clear he hadn't seen it rather than just chose to ignore it," said Coyle.
"I have seen the pictures. He clearly punched the ball. There was no disputing the ball was over the line but I thought we were playing volleyball."
Despite receiving a poor reception from the Clarets faithful, Coyle refused to be negative about his time at the helm.
"It is such a unique club and it would take something special to rival the passion these supporters have for their club," he said.
"I will never have a negative word to say about this football club. For two years I was a hero. Now I am a villain."
Source: PA