I have read and been told by several people that if you crate train at night time the puppy will not urinate in the crate because they respect their space and they do not want to lay in their urine or feces. However, our puppy has urinated every night we have had him and last night he had a bowel movement in the crate. He barks uncontrolably and usually its because he urinated in the crate. The crate is not too big or too small so Im not sure whats going on. I do give him a chance to urinate before going in the crate.
I agree, he is barking becuase he has to potty. let the poor puppy out to go. Take away his food and water a couple of hours before bedtime. Take him out for a potty right before bed. Put him in his crate, and expect to take him out at least once during the night. It depends on the lenth of time he is in there. If you do not want to do that, get an x-pen and put his crate and a potty area in that. He can go when he wants and still have his crate to sleep in.