Some protesting fans said they had flags taken away from them while others were shouted at and harassed.
Stadium security officials also confiscated T-shirts and other items displaying anti-government sentiments.
Protests have been sweeping Iran since the death of 22-year-old Mahsa Amini in September.
Ms Amini was arrested in Tehran by the morality police for allegedly not covering her hair properly and died in police custody three days later. The demonstrations spread across the country with people demanding changes such as more freedoms or an overthrow of the state, and the government has responded with a deadly crackdown.
On Friday - at Iran's World Cup game against Wales - some protesters had Persian pre-revolutionary flags snatched from them by pro-government fans at the Ahmad Bin Ali Stadium.
Insults were also reportedly hurled at some people wearing T-shirts emblazoned with the words "woman, life, freedom" - a phrase that has become a rallying cry among protesters against Iran's authorities.
One Iranian spectator alleged that Qatari police ordered her to wash off the names of protesters killed by Iran's security forces from her arms and chest after pro-government fans complained.
Another woman said she was prevented from wearing a T-shirt with Ms Amini's face in the stadium.
Women giving interviews to foreign press about the protests were also seen being harried by at least one group of men.
Some used their mobiles to film the women who were also subjected to verbal attacks and the men loudly chanting: "The Islamic Republic of Iran".
The match itself, which Iran won 2-0 against Wales, saw Iranian players booed and whistled at as they sang the country's national anthem before kick-off.
At their earlier game against England on Monday, the players remained silent during the anthem in an apparent expression of support for anti-government protests.Some fans in the stadium wore hats with the name of former Iranian football player, Voria Ghafouri, written on them.
A critic of Iran's government, he was arrested in Iran on Thursday and reportedly taken away by authorities after being accused of spreading propaganda.
Capped 28 times for his country, Mr Ghafouri was part of Iran's 2018 World Cup team and his absence from the 2022 squad surprised many.
The Iranian-Kurdish player has been a high profile voice defending Iranian Kurds within the country.
Earlier this week, the UN Human Rights Council voted to set up a fact-finding mission to investigate the crackdown on the anti-government protests in Iran.
The UN said Iran was in a "full-fledged" crisis and more than 300 people had been killed and 14,000 others arrested over the past nine weeks.
Iran dismissed it as an arrogant political ploy.