He definitely needs more space than a crate for long hours like that.  An ex-pen with pee-pads, his bed in the crate w/door open, plus food and water available.     
Their bladders are so small, and 12 weeks is even pretty early to crate train, unless you can take him out often.   
Since he can't hold it that long, he's going to eliminate in his crate even though he doesn't want to.... and eventually he'll get used to being soiled.   
My pups at that age had to pee almost every hour.  Pad training in a pen was good, but also I'm home full time.        |