Ignore it; ignore it; ignore it!
Ignoring the whining is the best thing to do (especially if you don't live in a condo or apartment where you have to worry about neighbors being disturbed). I'm of the mind that even if your dog appears to be barking in her crate because he needs to go to the bathroom, it is better for him to have an accident in her crate than for her to think that you'll let him out when he starts barking (I let him out pretty frequently to go to the bathroom, so there are very few instances when he's barking because he needs to go).
I know that with our boy, every time we let him out when he's barking sets us back a few days or so in his training (that is, even if we were making progress with him, he'll go back to his barking ways if he's even once let out while he's barking).
My wife and I have a rule that when he's been barking in his crate and stops, we set a watch or timer for 10 minutes, after which time we'll let him out. If he doesn't stay quiet for 10 minutes, the clock resets.
It has shown improvement, but we still need to work on it. |