Also if you are letting her free feed, you might try feeding twice a day at regular times and then removing her food. It's much easier to predict when she will poop if you're controlling her intake!
How big is her crate? If its too large they will go in the crate. 3 months is young! Bella is 4 months but she does great with her crate training, very few accidents.
I was born to be a pessimist. My blood type is B Negative.