Why would my 2 month old baby have mucus poop?

Normal: A small amount of mucus in stool is normal. See this site for information. http://www.mayoclinic.com/health/mucus-in-stool/an01296.

VIRAL INFECTION ?: If baby has viral infection like colds mucus can appear in the stools. Baby is fine when he is feeding good even if there is mucus in the poops.

Allergy or normal: If the baby is feeding well and there is no blood in the stool or unusual vomiting or other signs of illness, then it may be normal to have a mucousy stool from time to time. However, mucus may be a sign of allergy to a component of infant formula, or in some cases something in mom's milk. If this happens rarely, probably not a big concern. If frequent, consider discussing with pediatrician.