Don't Use Crate as Punishment
The idea for using a crate is to simulate the "den" environment. It is to give your puppy a sense of security, safety and a place to call his own. Therefore, it should never be used for punishment. The crate should have only enough room for him to stand up and turn around by blocking off any extra space inside the crate.
Overcome Whining from Crate Training
Whining is one of the common problems with puppy crate training. The puppy may whine to get out of the crate or to notify you that he needs to go outdoors to relieve himself. Do not immediately respond to his whining but rather stay nearby but ignore him. If he does not stop, reassure him in a pleasant tone. Finally, if he seems anxious he may really have to be let out of the crate to relieve himself. However, be careful never to reward whining or crate training will only become an unpleasant experience for both of you and prolong the learning process.