The Celtic goalkeeper's decision making was called into question against Slovenia.
Scotland's World Cup hopes were dashed as Gordon Strachan's side could only manage a 2-2 draw when all three points were needed to secure second place in Group F and put themselves in the hat for a playoff spot.
Celtic hitman Leigh Griffiths had fired the visitors into a 1-0 half-time lead but Roman Bezjak levelled up on 52 minutes by planting a header beyond Gordon who, in retrospect, could have perhaps come to claim the cross which led to the goal.
And former Rangers striker Thomson believes that the 34-year-old deserves a bit of criticism for failing come off his line.
"Possibly could have come off his line for Slovenia's first goal, the Celtic goalkeeper made a couple of smart saves in the second half," he told BBC Sport.
It was indeed a questionable moment from Gordon whose judgement also let him down in Hampden Park back June when the Celtic man was arguably culpable for at least one of England's goals in that thrilling 2-2 draw.
But the former Sunderland goalkeeper has had an excellent last few weeks at club level, pulling off some stunning saves against Ross County and Hibernian.
You can't question his reflexes, but his decision making seems a bit awry.