The map of Germany and the Low Countries Stokes and his men are bent over shows a map with the modern-day coastlines, including the Dutch province of Flevoland. However, the 1,000 square kilometer island only came into being in 1968 when it was reclaimed from the sea, long after the Second World War.
When the main characters are looking at a map of Belgium, the Netherlands and a part of Germany. The Dutch province 'Flevoland' is displayed as a part of the Netherlands. Flevoland however wasn't reclaimed until 1968, before that time it was a lake called the 'zuiderzee'.
The first mention of the Madonna is in connection with the Onze Lieve Vrouw Kerk. The church shown in the film, though, is a completely different one. Also, the Madonna is displayed in an altar piece, not standing on its own.
During live fire training, the location of the World War I memorial is attributed to Saint Louis, Missouri. The sculptor upon whom John Goodman's character is based designed sculptures for St. Louis' World War I memorial, which is called the Soldiers Memorial and should not be confused with the National World War I Memorial located in Kansas City, Missouri.
In the movie, it was mentioned for several times that the Madonna is stolen from the cathedral in Bruges. In reality, the Madonna is on display in the Church of Our Lady, not the cathedral of St. Saviours.
In front of the salt mine in Altaussee, they tell us that "this territory goes to the Russians". But in fact the whole area in Altausse belonged to the American occupation zone. The Russian zone was way further to the North and to the East.
When Matt Damon's character, James Granger, an Army officer, visits the apartment of Cate Blanchett's character, Claire Simon, he is not wearing his uniform but is wearing a casual, short-sleeve shirt instead. During World War II, it was a strict rule that members of the military had to wear their uniforms at all times, on and off base, even while home on leave. This scene, however, is in liberated Paris, 1944, and still considered a war zone. The casual attire of this character is seriously against military regulations during WWII, especially for a war zone.
One of the Monuments Men is taken for a ride on a biplane that has been hidden in a French barn. The aircraft registration number starts with a G, indicating that it was not registered in France, but in Great Britain.
The goof item below may give away important plot points.
When old Stokes comes back to Bruges to see the Madona in 1977, he can come close to the statue to view it. Since 1972, the statue has been behind bulletproof glass and the public can not come closer than 15 feet.