Usually if the crate is just big enough for the dog to turn, lay down, stand up, sit, etc comfortably.. they will not go in it.

A lot of the time if it's a larger crate they will go potty on one end and lay in the other.

Dogs usually shouldn't be left alone long enough so that they HAVE to go in their crates. Just take him outside to potty before you put him in it and when you take him out.