Blood in the stool is commonly caused by an allergy. Allergies can develop over time, so even if she didn't show signs before, it's possible that she is allergic now.
It's also possible for a breastfed child to have an allergy and show no symptoms. My son has several allergies (dairy, eggs, and nuts) and was exclusively breastfed till he started solids at 6 months, then I continued breastfeeding till he was a year old - he never had formula. He never had blood in his stool or any other indicators of a food allergy aside from eczema. But the very first time I fed him yogurt, he broke into full-body hives and vomited.
Anyway, my point is, allergies can vary in how and when they present themselves. I'd follow the doctor's advice for a couple of weeks and see if it makes a difference. I hope your baby is ok. If it does turn out to be an allergy, feel free to contact me for help in managing it. My son is 3.5 now and we've become pros at eliminating allergens from his diet.