Hi, vamosj,
It is really frustrating when this happens! If she is almost 3 months old now, hopefully it won't be much longer until she learns the crate is not for pooping.
After 3 months with our puppy (house dog) many years ago, my wife and I finally were about to give up, when all of a sudden, she started going outside!
Here is a site with some good information on housebreaking:
http://www.leerburg.com/housebrk.htm
It is important to be persistent. When you start to take her outside, always ask "Do you need to go?". She will soon get the idea. Then, if she goes, always praise her with "Good girl", or something similar.
Take her out before you need to leave the house, ask her the question, and keep doing it. Eventually, she will get the idea.
The above suggestions are from the link I gave you. I do wish you and she the best.