Puppy with separation anxiety goes potty in his crate?

The position of your crate is the problem. You have literally abandoned the pup. The crate should be where you mostly are yourself, during the days. Leave the T.V. or radio on, low, for some company for him. At night, move the crate beside your bed, where he can see you. If he starts to act up by your bed, you can just put your hand or finger in the crate, and he should calm down. Another thing is, you may be leaving him in the crate too long, as pups can't hold their bladder for long periods of time. Before you go out, or to bed, run him around for a while to tire him out. He'll then sleep mostly in the crate while you are gone. Don't expect him to be able to 'hold it' much more than 3 - 4 hours, at his age. Small breeds have small bladders, so can't hold it as long as a larger dog could. Is your crate too big?? It should only be as big as to put his water and food bowl in on one end, and a blanket on the other end. Pups, unless you leave them in the crate too long, seldom will dirty their 'den'. He should be able to lay on his blanket, fully extended, without touching the ends or sides. Give him a chew stick or toy to amuse himself. How about hiring a dog-sitter? You don't need to hire from a company, just ask any neighbours to let him out a few times a day, while you are out.