Add a few details: is this a puppy you recently got? What do you mean his breathing is "weird"? Is it labored, heavy? Are you crate training him?
Every dog I've ever crate trained has barked & whined in the crate at first. Of course they were puppies and they eventually would stop if ignored and placed in a room by themselves away from the action.
If your dog seems to be in pain while breathing or is having a hard time breathing, you may want to monitor him tonight and if it doesn't improve either call your vet or take a trip there to make sure it isn't anything serious.
