Continuity mistake: After the "car chase" the white car gets put in the barn. When the black car arrives it is covered in mud (so much they have to wipe it off the windscreen) from the dirt track. The white car only has a few specks of dirt.
Continuity mistake: In the scenes in Bletchley (south of England) it is obviously early Spring (daffodils, few leaves on trees), but towards the end of the film, and apparently only a few days later, when a German U boat surfaces off the coast of Scotland, it is clearly high summer, with all the trees covered in leaves. Trees don't come into leaf that quickly, and the seasons are always later in Scotland.
Factual error: Reference the rural scenes. In the 40s, barley fields did not exhibit large perpendicular tracks made by crop sprayers.
Factual error: At the end of the film, Tom Jericho makes his way to the "Adelphi Hotel" in Manchester. The outside of the Adelphi building just off the Strand in London is used.
Factual error: Kate Winslet and Dougray Scott drive through a field of the crop, rape. This crop was not grown during the second world war.
Plot hole: When the police search the white car and the barn they fail to find the compartment in the car behind the boot in which the decoding equipment was hidden. This is completely improbable. It was a standard car, the compartment was not a secret add on, and the police were supposed to undertake a thorough search of everything.
Other mistake: The last shots of Trafalgar square you can see twice a UPS van driving in the background.
Other mistake: In the 1946 Trafalgar Sq scene, modern double yellow lines can be clearly seen as being blacked out on the edge of the road.
Factual error: At the beginning of the film, as a British Admiral (or senior naval officer) leaves Bletchley he returns a salute. Although a naval officer, he does not give a naval salute but rather a half hearted army salute.
Continuity mistake: In the scene in Scotland where Puck is rendezvousing with the German submarine whilst being watched by the British security services and police, there are several shots of the sub through binoculars supposedly from the perspective of the British on top of a hill. These views are all (with the exception of the last one of Puck meeting the sub) from sea level.
Factual error: The scene of 1946 London - Trafalgar Sq. looking south down Whitehall. You can see the turrets of the new MP office building - put up only a few years ago.
Factual error: A scene labeled as being from 1951 shows a name (Nook) having been typed on paper and then being whited out by a substance similar to Liquid Paper. Liquid Paper wasn't invented until 1956 in an American kitchen and wasn't marketed, and the patent applied for until 1958. (00:20:01 - 00:20:25)
Factual error: In the opening scenes the staff car door is opened by a four-ringer Wren (Deputy Director, very rare) equivalent to Royal Navy Captain, instead of a rating.
Chosen answer: This is not a mystery. Claire "stole them to read them" as Tom Jericho told Hester. As he later explained to Wigram, she had taken the messages to give to Puck who had the means to decipher them, and who was looking for his missing brother. The Kestrel traffic from ADU contained the names of victims of the Katyn Massacre. However, Puck and Claire were surprised by the imminent reappearance of Tom, and suddenly fled, explaining why some messages were left behind.