Continuity mistake: When Briony sees Cecilia coming out of the fountain (from Briony's perspective), Cecilia steps out of the water with her right foot first. When we see the same scene afterwards, from Cecilia an Robbie's perspective, Cecilia steps with her left foot first.
Factual error: Near the beginning of the film before James McAvoy heads up to the house for the evening meal, he is seen looking up through a skylight when a Lancaster bomber slowly flies overhead. At the time it was was supposed to be 1935. The Lancaster bomber did not fly until the beginning of 1941. And if it was supposed to be an Avro Manchester, then they only had two engines.
Continuity mistake: In the first enactment of the fountain scene from Briony's viewpoint, the twins have just left her room and can be heard yelling downstairs for Celia's permission to go swimming. In an immediate, steady shot she goes to the window and witnesses the fountain scene already midway through. As we see in the next scene, from Celia's perspective, the twins run by asking to go swimming and she lingers in the piano room for several minutes and takes even a few more minutes chatting and walking with Robbie before they even begin the fountain scene.
Revealing mistake: During the long tracking shot at Dunkirk, steadicam operator Peter Robertson had a little assistance in getting around. This took the form of a kind of golf cart (from the beginning to just after shooting the horses), and later a rickshaw (from little after the choir to just before the steps ascending the billets). If you look at the ground to the left just as the camera begins backing away from the carousel, you can see tracks in the sand made by the rickshaw. Keep watching the sand near the actors' feet to see more.
Continuity mistake: In the scene by the fountain from Briony's point of view, when Cecilia takes her top off she pulls the strap of her undergarment twice. However, from Robbie's point of view, she doesn't pull the straps at all.
Factual error: The early scenes in Atonement take place, according to the opening caption, in "England 1935" on a single summer's day. The action shifts at the beginning of scene 9 to "Northern France four years later" according to the caption. This, then would have been the summer of 1939 when Britain wasn't yet at war. The Dunkirk retreat took place in the summer of 1940, five years after the action in scenes 1-8.
Factual error: In the section of the movie set in 1935, there is a scene where Robbie is daydreaming and the image of a four engined bomber crosses the screen. The image is of a Short's Stirling (the tail configuration is markedly different to the Lancaster), an aircraft which did not enter service until 1939.