Can you leave a video recorder on to see if your puppy is experiencing anxiety when left alone? Probably it's the only way to know for sure. How much exercise is she getting before you crate her? Are there certain times a day that she usually eliminates? Would these be the times that you sometimes have to leave her? By any chance, do you know her prior history? Perhaps she was kept in a crate for too long periods of time when she was just a wee puppy and learned that it was ok to potty there?
If she never has accidents in the house, you might want to consider leaving her in a safe gated area. Perhaps a kitchen or a spare room that's been perfectly puppy-proofed.