Factual error: The Lyceum Theatre, referenced in the film, did not exist in 1828 as it was not built until 1834.
Factual error: William Burke did not confess to the crimes in order to save his friends and love, he was in fact betrayed by William Hare who sold him out after they were caught.
Factual error: When Burke and Hare stop for a drink and Burke says that they have no money, Hare plucks a half-crown from underneath Burke's cap. The half-crown that is used in the film is from 1902 - 1910 which is nearly 100 years after the film is set.
Factual error: Near the end of the movie there is a high shot of Market Square, which is supposed to be below Edinburgh Castle as established during the opening scene of the movie. However the view looks almost identical to the Royal Mile which runs from the Castle itself down to Holyrood Palace. You can even see the spire from St Giles Cathedral in the background, which is on the Royal Mile.
Continuity mistake: In the "multiple dissection" scene Doctor Knox uncovers each of the four dead bodies one at a time. But, following a quick edit to the applauding students, in a closer shot one of the bodies is covered up again.
Other mistake: When Burke & Hare chop down the tree to stop the coach, they hit the tree with their axes at chest height. When the coach approaches they have hardly made a dent in the tree and when they push to tip the tree over, it doesn't break at chest height, but the entire tree falls, arguably still fully intact.
Factual error: Greyfriars Bobby wasn't born until the mid 1850s. Burke and Hare were robbing graves and murdering twenty-five years earlier.
Continuity mistake: When Lucky makes her husband some dinner, she puts it down in front of her husband - and only that. In the next shot when she backs away after putting the plate down, there is a small pot of flowers there that weren't in her hands in the previous shot.
Factual error: On the opening shot of Edinburgh Castle, you can see the spire of The Hub to the left of the screen. The film takes place in 1828 but The Hub was not built until 1845.
Factual error: Two hangings are shown in the film, in the style of a "long drop" designed to break the neck and cause instant death. This style was first introduced in the 1870's by William Marwood as a more humane approach. Before then, and certainly in 1828-1829 when the film was set, the victim was simply suspended by a rope around the neck, and choked to death by suffocation.
Factual error: When Ginny visits Burke before his execution, they spent so much time together that we see two candles burn almost all the way down to the bottom. Candles take several hours to burn, and in reality, nobody would be able to visit a condemned man for that amount of time. Even if it's for only 2 hours or so.