Eva Peron's shoes change during the waltz scene with Che. Apparently Madonna began filming with higher heels, fell, and, fearing for her unborn baby, switched to lower heels with a clearly different strap set-up. Her hair also changes.
When Eva is in her bed towards the end of the movie, she has blue eyes.
The fan behind Che during his first song in the bar.
Evita's right arm position when she's listening to Magaldi singing.
The glass cover over the croissants on the bar counter to Evita's left.
After Evita & Juan Peron are married they walk outside the church and there is an army of well wishers and photographers who snap their picture. In real life Evita and Juan were married with the most absolute secrecy with the only guests being Evita's mother and one of Peron's ministers. Certainly no photographs were taken at the event.
In the film, Agustin Magaldi performs at a charity concert for victims of the 1944 San Juan earthquake, and briefly re-encounters Evita backstage. In real life, Magaldi had been dead since 1938.
The cup in the church when Evita faints falls to the ground, yet it spills no wine.
Madonna's pregnancy shows during early interior scenes in Evita's home town and the bar in Buenos Aires, but disappears in exterior scenes, which were shot earlier.
During the Mass, when Evita is receiving Communion, she responds to the priest with "Amen". However, in a Tridentine Mass, nothing is said by the communicant before receiving the sacrament. The practice of saying "Amen" does not begin until the Second Vatican Council.
When receiving Holy Communion Evita partakes of wine, a practice not permitted until the Second Vatican Council (1962-1964).
When Evita first arrives in the city, distant shots of the skyscrapers show modern microwave antennas atop the buildings.
During a parade/riot set in 1943, an armored car is seen. The make/model is a Daimler Fox, not manufactured until the 1970s.
During "A New Argentina", the singers walk through a shipyard. The cranes that they walk between are container ship cranes that wouldn't have existed before 1952.
During the second shot of the soldiers in the shower during the song "Peron's Latest Flame", the lip movements do not match the words spoken.