Many dog owners use puppy crate training as part of a housebreaking routine, as the crate satisfies the dog's desire for a closed-in space, like a den. Crate training may be associated with separation anxiety, but the crate does not necessarily cause your animal's anxiety.
Separation Anxiety More Common by Breeds
Rather than chalking up your dog's anxiety disorder to crate training, bear in mind your animal's breed. Separation anxiety is more common in certain breeds of dogs, and especially those who form deep bonds with their owners, like Labradors.
Don't Reward Bad Behavior
Your puppy will be nervous whenever left alone for the first few months simply because he or she is not used to solitude. Don't feel guilt about leaving the puppy in the crate; wild dogs generally live in a similar environment, so putting your puppy in a crate is equivalent to putting your puppy in its home.
Don't make a fuss when coming home to your dog, especially if he or she has behaved poorly in your absence. Reassure them, but don't give the impression that the dog will be rewarded for whining in order to get attention. However, make sure that the puppy associates the crate with positive things, like favorite toys and puppy treats, since this will encourage him or her to enjoy their time spent crated.