If he is pooping when you close the door, it is because he is terrified; he may never have been put in a crate by himself before. He has just been taken away from his mom and sibs, he may never have been alone until he got put in a crate on a plane.
I assume you are making sure he is empty before you put him in the crate right?
Right now, I would not close him in a crate, because he is making associations right now that you don't want. He is terrified when you close the door, because it means you are leaving. He is also "practicing" eliminating in his crate; and he is probably learning that you whip him out of there as soon as you notice the poop (it would be cruel not to). So in time, he may think 'hey, I poop, she gets me out'….right now, I think he is not having a thinking response, just a panicked one.
Soooo....what I would do is two approaches. Get an X-pen to keep him in when you have to leave, put his crate in it open, and some nice toys, and whatever else you think he would like to play with. Then have training sessions for leaving: put him in his X-pen, give him a nice treat, and walk out the door, stand right outside the door, and come in BEFORE he starts crying. If you can't do that and he starts crying right away. Come back in and ignore him until he is quiet, and let him out.
Then with the crate, have training sessions. Put some really yummy treats in there, but keep the door closed. Show him, and get him reved up to go in. Open the door, and close it behind him. At first just let him stay in there until he looks uncomfortable, but BEFORE he starts to carry on. Then let him out while he is quiet and clean. At first you won't leave his sight. Later as he starts to feel more comfortable you will leave and go to another part of the house, and then walk back. The goal is to not let him freak out.
IMO, this puppy is more upset by the separation, than the crate, but he has a scary association with the crate; you need to build trust in this puppy that you will come back...but that is not unusal. It is going to be more work than you probably thought it would be...but let me tell you....I wish I had done this with my crate screamer as a puppy. I took the route of just letting him scream it out, and never let him out while he is screaming (he never defecated)..and he STILL hates crates, at 8 years old.
Best of luck, and please let me know if any of my directions were confusing...I haven't had any coffee yet