Decidual bleeding: This is a common cause of vaginal bleeding or discharge during early pregnancy, including at 12 weeks. It occurs due to the separation of the decidua (the uterine lining) from the embryo. The blood may be dark brown due to its age.

Threatened abortion: This condition is characterized by vaginal bleeding or discharge during the first 20 weeks of pregnancy, without cervical dilation. The discharge can be dark brown if the bleeding is intermittent and the blood has had time to oxidize.
Cervical polyp or erosion: These conditions can cause irregular vaginal bleeding or discharge, which may appear dark brown.
Infection: Infections such as cervicitis or pelvic inflammatory disease can cause abnormal vaginal discharge, which may be accompanied by other symptoms like odor, itching, or fever.

Ectopic pregnancy: Although less likely at 12 weeks, an ectopic pregnancy can still present with vaginal bleeding or discharge. It is crucial to rule out this condition due to its potential for severe complications, including rupture and maternal death.
Molar pregnancy: This rare condition can cause vaginal bleeding or discharge, often accompanied by other symptoms like excessive uterine size or severe morning sickness.
Placenta previa: This condition, where the placenta covers the cervical os, can cause painless vaginal bleeding. Although it typically presents later in pregnancy, it's essential to consider in any case of vaginal bleeding.

Choriocarcinoma: A rare type of gestational trophoblastic disease that can cause vaginal bleeding or discharge.
Uterine rupture (in a scarred uterus): Although extremely rare at 12 weeks, uterine rupture can occur in women with a previous uterine scar, such as from a cesarean section. It is a life-threatening emergency.