The location of Jane's cottage was so isolated that there was no mobile phone reception. A member of the crew had to be stationed in a nearby phone booth with a walkie talkie in case the crew needed anything - he didn't complain, however, as the local residents brought him tea and biscuits throughout the day.
While the majority of the book takes place in the 1830s, director Cary Joji Fukunaga changed the time-line so that most of the film takes place about a decade later, because he felt that mid-1830s fashions were very over-the-top and unflattering, and wanted to dress Mrs. Reed in those styles rather than Jane Eyre.
Director Cary Fukunaga chose not to film any footage of Thornfield Hall burning down because he wanted the film to feel like the novel, which is entirely first-person from Jane's perspective. In the book, Jane is not present for the fire, and Fukunaga didn't feel there was a way to include it organically in the film.
Romy Settbon Moore, who plays Adele, was cast in part because she speaks fluent French; Cary Fukunaga held auditions at a local bilingual school to find a girl who could convincingly play a French child but who could also understand his direction.
This is possibly the first adaptation of Jane Eyre in which her rival, Blanche Ingram, is shown as described in the book: a striking black haired woman. In most other adaptations, she's played by women with bright blonde hair, likely as a contrast to dark-haired Jane.
During the scene where Mrs. Fairfax, Adele and Jane are eating while Mr. Rochester is shooting birds, Cary Fukunaga would play music in ear pieces that the actors wore to make them react to the gun-shots. At one point he forgot that Romy Settbon Moore was on set and played a song with explicit language, causing Romy's Mother to scowl at him.
Cary Fukunaga wanted a scene to illustrate how much Mr. Rochester's presence at Thornfield Hall disrupted the lives of its permanent residents, so he wrote the dinner scene, in which Mrs. Fairfax, Jane, and Adele try to carry on a conversation while Mr. Rochester fires a gun right outside the window. This scene does not take place in the novel, and in the film's commentary Fukunaga claims it was the only original scene written for the film.
The logo for the popular movie website Gordon and the Whale (owned by Chase Whale) appears towards the end of the movie as a watercolor painting. Director Cary Joji Fukunaga discussed this in an interview with MakingOf.com
While shooting the climactic post-wedding scene between Jane and Rochester, filming had to be stopped repeatedly because Michael Fassbender's suspenders (British: braces) kept breaking and had to be re-sewn.
When Adele tells Jane about the ghost that haunts the house, there is a doll dressed in white in the top window of her doll house. This foreshadows events later in the film, since the ghost is actually a mad woman dressed in white who lives in the attic.