The defenders thought one way and the attackers another. "Well, if you can't decide-" he said to them. Within the rules of the game, decisions by match officials will always be subjective, but referees might still feel under siege.
In recent weeks, Kenny Shiels, the Kilmarnock manager, has claimed that some decisions against his side are personally motivated against him, while Steve Lomas has begun an eight-match touchline ban. After last weekend's Dundee derby, Barry Smith questioned two of Willie Collum's decisions, and said yesterday that following a discussion with the referee, they would have to "agree to disagree".
After undergoing his FIFA medical tests at Hampden yesterday, Thomson addressed the relationship between managers and referees, the feeling there is a growing divide between them, but also the accusation that match officials are aloof. He was spirited, without being defensive, and the sense was of managers' complaints being put firmly in perspective.
"What am I going to say that is going to persuade these managers it's not personal?" Thomson said. "Our job is to apply the laws of the game to the best of our ability. There is a possibility that it's a deflection tactic at times. But it's disrespectful and disappointing that managers would think that because nothing could be further from the truth than we go to matches and think 'I don't like this manager, I'm not giving his team anything'. You wouldn't be a top referee if you went into games with that attitude.
"Some comments certain managers have made are comments they will regret. Because I don't think what they said benefits the game. We are happy to speak to any managers or any players to explain the laws of the game to them. We have done that and will continue to do it. If they want to speak to us we will go in and speak to them because the best time to speak to players and managers is outwith the game. During the game the environment is emotional."
The Scottish Football Association ran a Whistleblower section to their website between in 2007 and 2008, allowing referees an opportunity to explain or react to decisions. Thomson used the initiative to admit that he would have awarded a penalty to Celtic during an Old Firm game at Ibrox had he been in the position to see the foul on Shaun Maloney from the same angle as the television coverage. Yet Thomson felt his honesty was then constantly held against him, with the admission being referred to every time his name was mentioned in the media. "I thought, what's the point, why am I sitting here being the only person in Scottish football holding my hands up," he said.
The experience with the Whistleblower strengthens his view that the best way for referees and managers to deal with contentious decisions is to talk about them. Thomson does not believe, for instance, that referees should speak to the media after matches, but is happy to talk to managers, so long as they wait until the end of a 15-minute period after matches during which the SFA have asked for match officials to be left alone, and so defuse any tensions.
"We know how emotional the game is and know which coaches are going to be upset over certain decisions," he said. "So we say to them to wait 15 minutes then come and speak to us if they want an explanation. We don't want these things played out in the media.
"We ran a campaign last year when we went in and spoke to every single SPL manager and player and every SFL manager. That benefits us because it lets them understand what our views are and how we interpret the laws of the game. So it did surprise me when I read managers saying we were too aloof recently. Because our door is always open. Nobody is going to hide behind any decision we make on a Saturday."
Along with Collum, Thomson is one of Scotland's two FIFA Elite Referees, and he is also on the 19-man shortlist of referees for the 2014 World Cup. England, with 10-times the population, have only three Elite Referees. "We're kicking well above our weight," Thomson said. "I would say we're at the highest level [of refereeing] we've been at."