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Thomson's foot made contact with the exposed head of Scotland flanker Alasdair Strokosch in the 45th minute of New Zealand's 51-22 win on Monday morning.
The 30-year-old was sent to the sin bin by French referee Jerome Garces on the advice of Irish touch judge Simon McDowell.
Hansen anticipated the incident would be reviewed and hoped Thomson's intent would be considered.
"I don't think it was a stomping personally but it's not for me to decide," Hansen told journalists.
"Someone will look at the game and make a decision whether what he did had malicious intent or whether it was reckless. I'd suggest it will probably be reckless.
"It looked like he got frustrated because someone was lying on the ball and he placed his foot on the guy's head. He didn't stomp him, which was one good thing."
Scotland coach Andy Robinson responded in the affirmative when asked if a boot to the head should result in a red card.
However, Strokosch said he was happy with the sanction imposed.
"It certainly wasn't malicious. There was no damage done. He barely grazed it," the Scotland No 6 said.
"I would say the yellow card's fine. I wouldn't take it any further. It wasn't a big deal."
While Thomson's availability for the remaining three tests of the tour is in doubt, it is also unclear where he will play his rugby next year.
The 29-Test Otago loose forward hasn't signed a Super Rugby contract for 2013 but he is also yet to secure an offshore deal.