Pooping in the crate is a sign that the crate is too large. My "Puppies for Dummies" book said that this is the number one sign that you have a crate too large for your puppy.
But your pup is young. I would fully expect this to go away as your pup grows into the crate and gets better control of body functions.
Here's a great page on Crate Training info:
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Be certain that your puppy has fully eliminated shortly before being crated. Be sure that the crate you are using is not too large to discourage your pup from eliminating in it. Rarely does a pup or dog eliminate in the crate if it is properly sized and the dog is an appropriate age to be crated a given amount of time. If your pup/dog continues to eliminate in the crate, the following may be the cause
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http://www.inch.com/~dogs/cratetraining.html