Most puppies won't foul their crate or other sleeping place. I am placing more and more blame for the ones that do on poor care by the breeders. I am afraid there are many people breeding puppies that are utterly ignorant of the care and socialization puppies need after they are whelped. I see many questions from would be breeders indicating they have never read a book on dogs and certainly not one on breeding. They fail to realize the importance of allowing the mother and puppies to keep themselves clean. They also hold the puppies past 12 weeks until they no longer accept new things well.
Undoing such abuse is tough. Start by reading the sticky at
https://www.askmehelpdesk.com/dogs/i...tml#post251809 While I mention putting the puppy back in the crate if it doesn't go, I really think you need to pay close attention to the puppy, recognizing when it needs to go out. Then, while you have it out, don't let it sit. Make it move around. They can't walk and hold it very long.
The grid I mention in the sticky goes a long way toward keeping the puppy dry, but is less effective on stools. The cleaner you are able to keep the puppy, the more likely its instincts for cleanliness to recover.
I think part of the problem is the stress of being left alone. At least a 9 week old is young enough to learn quickly. You can always try leaving a Kong filled with peanut butter in the crate. Just don't over do it. A little peanut butter is OK, but most of its calories need to come from a complete and balanced dog chow.
If you go out with the puppy, you can call it out into the grass and then praise it for eliminating there rather than places you want to keep clean.