The title has multiple meanings
From an interview with CinemaBlend:
Edwards told Empire [magazine] that the main idea for the title (which occurred to him last month) was to distinguish how this Star Wars movie is the first of the franchise to not be connected to the main saga. He explained:
I'd been thinking about it. What does it mean? 'Rogue One' is a military call sign to some extent, but this is the first film that's gone off-piste and is not part of the saga -- or the Anakin story -- so it's the 'rogue' one, you know?
However, Rogue One wasn't just given that title to highlights its differences from the previous Star Wars movies. Gareth Edwards also noted how the title refers to main protagonist Jyn Erso and her "rogue streak," specifically how despite her drive to do the right thing, her guerrilla tactics end up causing a lot of destruction. He continued:
It's kind of describing her as well in a similar way. It has [all] these split, multiple meanings that made it feel like the right choice.