Honda was hit with a $5000 fine after complaining that Japan's opener against Palestine was "like playing basketball".
And Queiroz was fined $3000 following his criticism of Australian referee Ben Williams in Iran's 2-0 win over Bahrain.
"I was not happy because after nine, 10, 12 fouls, stopping the game systematically. The referee must take action," Queiroz said after the game last week.
Queiroz was later told to steer clear of talking about referees and he reacted sarcastically when told to avoid the issue at an official press conference.
"It's clear even if you talk politely, with respect, education, calm, cool, you're not entitled to talk about the referees," said the former Real Madrid and Portugal boss.
"After 32 years of my work in football I was never told I cannot give an opinion about the game. Maybe it's only because of the sponsors."
However, Oman coach Paul Le Guen escaped any punishment for his comments over a penalty appeal in his side's 1-0 defeat by Korea Republic.
Refereeing standards have long been a bugbear of Asian football but a determined improvement drive by the AFC has yielded results.
However, inconsistencies remain and at last year's FIFA World Cup, Japan's Yuichi Nishimura was slated for awarding a soft penalty in Brazil's first game against Croatia.
After the AFC Champions League final in November, Nishimura again came under fire from Saudi club Al Hilal after it was denied a number of strong penalty appeals in its 1-0 loss to Western Sydney Wanderers.
