My puppy is 9 weeks and I have had him for 3 days he soils in his crate at night is this common and how long does this last and is there anything I can do.

At 9 weeks you can't really expect much, and even more so as he is still settling in at home.

What breed is it and what size crate are you using?

For most breeds you will need 2 crates... one for when the dog id a puppy and another for when they are an adult.
A lot of people make the mistake of buying a crate that will be large enough for the dog when it is fully grown.

A crate should be just large enough for the dog to comfortably stand up and turn around in, no bigger.
Dogs try to keep themselves clean and do not usually soil their bedding so by limiting the space inside the crate they see it more as a bed than a small room.