"We strongly condemn any attempt to wrongly use tickets reserved for disabled members of the general public," a FIFA spokesman said on condition of anonymity.
"FIFA asks fans to be respectful and only request these seats if they qualify for them."
The most controversial picture shows the back of a fan wearing Brazil's yellow team jersey at the Castelao Stadium in the northeastern city of Fortaleza, standing and applauding in front of the wheelchair.
The photo was apparently taken during Brazil's 0-0 draw with Mexico on June 17.
But the two teams had played at the same venue during last year's Confederations Cup tournament, when Brazil won 2-0.
The picture sparked a debate on Twitter, with one Brazilian user sarcastically questioning the "great miracle," while others noted that some disabled people can stand up some times.
Brazilian law has set aside at least one percent of World Cup tickets for people with disabilities.
FIFA said that people buying handicapped seats must show a medical certificate when picking up their tickets. More checks are conducted on game day.