Your puppy will whine at first because they don't like to be left alone. Dogs are den animals and the kennel or crate will become a place they feel comfortable.
If you let the dog out when it whines, it won't take long for the dog to catch on to that behaviour. A lot of people cave in to their dog when it whines because they feel sorry or guilty for their pet. Pretty soon, the dog is the one in control.
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