If he is actually chewing his nails then I can't see anything wrong with that. One of my dogs has been manicuring his own nails for 8 years and does a better job than me...
However, if your puppy is also licking his paws then he is probably itching, which could be an allergic reaction to food, dust mites, grass etc
If he doesn't lick then he probably simply doesn't like the angle you are cutting his nails at ;-)
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