#1: Your pup is using the toy just like she used the blanket. No surprise there.
#2: She's not stubborn, she's a PUPPY! Stubbornness requires a knowledge of what you want and deliberately going against that. She doesn't know any of your human rules yet, so she cannot be stubborn. Don't forget that "don't pee in the house" is a human rule.
#3: It's dangerous to leave something a puppy can ingest inside their crate with them when you aren't around. This goes double if the toy had a squeaker, since those can cause major problems if they are eaten. If you want to leave her a toy, get her a hard rubber toy like a Kong.
Did the vet do a urine culture to determine that she had a UTI?