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.
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.
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.