When the sisters tell Babette that the General will be coming to the French dinner, the driver who eventually brings that General to the house is already sitting in the kitchen.
In the church, behind the pastor there is a crucifix on the wall. While many Calvinist Puritan churches have no such images, there is variance among Protestant churches; as the pastor named his daughters after famous Lutherans, his church will clearly be more Lutheran in practice, thus allowing such images. At the time Denmark would have been predominantly Lutheran, and it is still the largest fraction among people registering as religious.
The Wires and sticks moving the big turtle in the kitchen are visible along both front legs, indicating it is a puppet/animatronic.
In 1871 Babette pays with skilling, which was the currency used at that time; 14 years later, Babette still uses skilling, but Denmark changed the currency in 1875 from skilling to kroner and orer.
Center-back zippers can be seen on many women's gowns. Most notably, on the white gown of the Swedish Lady-in-Waiting. The film is set in the 1800s. Commercial zippers were not used in apparel until the 1930s, initially in children's clothing.