Hormones can do that and she's about the right age. The presence of other rabbits can make hormonal behaviors more pronounced. How many other rabbits do you have? Are they housed separately? In same room?
Cage aggression is another thing that some rabbits get. If you are reaching into her cage to pet her when she tries to bite, she is likely protecting her territory. She should not be pet inside her cage but only when out for her daily exercise.
Any chance she's older and could be pregnant? If you are certain she's only 3 months old, then it could be hormones like Blue eyes said, or if there's any chance something happened to her that scared or may have hurt her, that could cause unexpected aggression. Could she have been accidentally frightened or injured, or do you have any children in the house that may have accidentally done something to her?
It might also be that separating her from her friend could be causing insecurity and the aggression in her, since the aggression started about the same time you separated her from her friend. If their cages/areas aren't next to each other, you could try putting them next to each other so they can see each other. That may help. You just need to keep a space between them or small mesh, as some males have been known to be able to mate between cage bars with wide enough spacing to make contact.