Again, I would not punish your puppy in any way for barking/crying/whining in the pen. You will only teach her to dislike the pen more. Ignore her when she's noisy. Noisy dog = invisible dog. Quiet dog = best puppy in the whole world! Shower her with praise and treats when she is quiet.
If she starts barking in other situations, you can then worry that she might become a yapper and we'll try to offer more advice at that point.
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