I'm not sure if this is the case with you or not, but I had the same problem with my puppy for several months before I was able to figure out that the defecating in the crate was not directly due to nervousness. I also tried reducing the crate size, etc. I would take him out a couple times, watched him go, before leaving and would come home to find a mess every single time (regardless of what treat I would put in there)…in addition to him screaming... I finally was able to figure out the problem. I take him out once, but in addition to that, I have to take him out for a walk shortly after that first time (he'll only go a second time if we're well away from the house and down the street). This only happens in the morning. In the afternoon he has no problem holding it .... the "crate anxiety" hasn't gone away completely , but there are no messes to clean up (which is helping reduce his anxiety day by day). Thought I would share my example, since I kept stumbling on " some dogs can't tolerate crates" and "signs of separation anxiety" when I was looking for an answer. It might be something that doesn't fit the norm. The clue for me was that he only pooped in his crate...I rarely found urine.