Whan said he was at home screaming at his television set when officials docked Thompson four strokes during the final round of the year's first major at Rancho Mirage, California.
"It's a great example of something that's 100 percent right by the rules and feels 100 percent wrong on all functions," said Whan, speaking at the StubHub Leaderboard event on the eve of the men's U.S. Masters.
"The penalty in this case doesn't fit the crime and it drives me crazy."
Thompson had six holes to play when her three-shot lead was wiped out by penalties for infringements committed the previous day and brought to the attention of officials by an e-mail from a television viewer.
The 22-year-old American, who went on to lose in a playoff, incurred a two-stroke penalty for playing her ball from the wrong place and an additional two strokes for signing an incorrect scorecard.
"When you see an athlete putting herself in the position to be at the absolute pinnacle of her sport and have a career-changing win and have it change like that, it's hard not to be a father in that moment," said Whan.
"And that's what I was. I was a father screaming at the TV, crying with my wife that night when I went to bed."
Under golf's rules, if anybody gets in touch and says they witnessed an infraction and video evidence is available, a review must occur.
"The belief ... is any input you get to protect the 144 players in the field, you have a right to make sure that you are protecting them. So that's what we do," said Whan.
"In this case our rules official saw this, it was an infraction and unfortunately we don't get to choose what kind of penalty to dole out. That's delivered by the rules of golf."
(Editing by Nick Mulvenney)
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