The note given to Abby Borden saying that a member of the Churchill family was ill did not actually happen. Lizzie, in her many iterations of the events of that day, said she believed Abby Borden was not in the house having a received a note that someone was ill. Abby was not upstairs changing her dress to go out at the time of her murder, she was upstairs making the bed in the guest room. She was on the side of bed closest to the dresser when she was attacked from behind and given the angle and severity of the blows to her skull, it is likely she never even saw her attacker.
In the beginning of the movie, Abby is shown telling Bridget that she'll be referred to as Maggie, but it was actually Lizzie Borden and her sister, Emma, who insisted upon calling her the same name as the former maid.
Abby Borden was killed in the guest bedroom while cleaning the room after John Morse's overnight visit, not in her and Andrew's bedroom.
The Borden house is shown to be a mansion. In fact the real house was (and still is) a very modest home that didn't even have indoor plumbing.
At the beginning of the movie, Lizzie goes to the theatre to see Catalani's opera "La Wally". The movie action takes place in 1892, the same year "La Wally" was premiered at La Scala, Italy, but was not premiered in the USA (New York) until 1909.
When Lizzie kills her stepmother, her armpits are cleanly shaved. Women in the US did not being shaving their armpits until about 15-20 years after the murders, when a new style for short sleeved dresses lead to women being encouraged to remove "unsightly" underarm hair.
The end of the film states that Emma and Lizzie had a rift "soon after" the trial and became estranged, but it was actually 12 years later that Emma separated from Lizzie and moved out of their house forever. No one knows for sure what the rift was about, but it's believed by many that Emma discovered Lizzie really was guilty of the murders.
The movie depicts Bridget Sullivan starting her employment with the Bordens 6 months before the murders. In fact, Bridget had worked for the Bordens 2 years and 9 months at the time of the murders. This comes out in her inquest testimony.
Andrew Borden wore a beard. Jamey Sheridan is clean shaven.