Hi
I had posted a question a while back about my puppy going to the bathroom in her crate, too. Everything that I've done to this point only helps for a few days, then she's right back to her old ways. I've switched her food, gotten her on a good feeding schedule, and have even created a "dog room" for her and my other dog to share so she is never alone. We've left the radio on, lights on, etc., and nothing has solved the problem. She is crate trained, but I also tried leaving her in the bathroom during the day - she shredded the toilet paper, tissues, trash, and smeared poop all over the walls and floor. What a MESS! Have also tried just leaving her in the dog room with the other dog, but she still finds things to chew up. So, she's back to her crate while alone. I am going to try the DAP diffusors (like Feliway for cats, but this is for dogs) - it's supposed to help calm anxious dogs and help with their behavior problems such as going to the bathroom inside. I love Feliway, so I'm hoping this helps. We also have a PhD dog behaviorist in the area, and I'm planning on getting her out for a home consult soon. If I can't get this resolved, she's going to have to find a new home! It is very frustrating having to scrub a crate (and the walls and floor around it) and bathe a dog every day!
Sorry for the news of my bad experience, but it seems there isn't anything easy (or cheap) to do to help with this problem!
Good Luck