When a dog whines during crate training, take steps to prevent its recurrence, such as keeping the dog in the crate until it has stopped whining. If the dog is released while it is complaining, it learns to whine for release.
Letting the dog out reinforces poor behavior and encourages the dog to continue. In addition, since crate training time builds gradually over time, whining sometimes signals that the dog has been pushed too quickly. Reduce subsequent crate times slightly.
If a puppy whines at night, it is possibly signaling a need for a bathroom break. If the whining does not stop after being ignored for several minutes, a quick trip outside is in order.