When you are showing your puppy to the crate or confined area for the first time, they may soil in the space due to nerves.  This is usually a one- time response due to all of the changes in their life.   They are just scared and this is very normal. Don't make a big deal out of it. Instead just clean it up and let's start all over.
 
The puppy needs to be in a space small enough to be comfortable but too small for them to soil.  A puppy will not naturally poop or pee where they live.  This is one of the keys but If they are given no other choice, they will. That is why it is so important to get them on a routine of feeding and eliminating.  Use a crate, play pen, or some form of fencing or gate that creates a small enough space to hold a bed.  Initially, you may also opt to use a towel or something that is easily washed. Housebreaking a puppy starts off with knowing their limits.