My girlfriend took a plan b 3 weeks ago and the first week she had brown discharge and then today she had another brown discharge (dark) reason?

Likely her period: This sounds like her period starting with the second bleeding, however a pregnancy test is recommended.

Plan B: Morning after pill( Plan B) when taken within 24 hours after intercourse can reduce risk of pregnancy up to 95%. In your case, even though she had brown discharge, it will be helpful to know your girl friend LMP, time of the intercourse and when the plan B was taken for a more specific advise. For any further questions, please see your doctor for pregnancy test. Good luck.