i'm not sure if this is a health issue or not, could it be stress from being inside her cage all night? we're clueless as to what we can do..any suggestions would be greatly appreciated !
Wait it out. I think it's a puppy thing. We used to have the same exact problem with Levi. We were always getting up at 12, 3, and 5 AM, giving the poor bugger a bath and washing his crate out.
If you've been giving her treats, I would stop for awhile and see if that makes a difference. The only food that didn't give Levi the runs was Puppy Chow. NOOO people food, I noticed that would make it extra bad. Also no doggy treats, no rawhide, nothing except water to drink. (My dad gave Levi a little bit of milk once... oy vey it was awful that night).
I would say Levi started to get better by 4 or 5 months, and after 6 months he was totally better. He's never pooped in his crate since 6 months I think.