My 12 week old baby had brown mucous in her loose stools. is that normal?

Hard to tell: It would be unwise to interpret your baby's mucus solely without looking at the entire picture. You may need to provide more detail as to how else your baby is doing - fever, feeding routine, blood present in stool, presence of pain, change in urination etc.? Brown mucus w/out other symptoms, otherwise, may not be something to worry.

Maybe: It could be normal if it occurs only once or twice. If it continues, baby should see the pediatrician to evaluate for infection or cow milk protein allergy.