Probably bug bites(maybe bees) or an allergy. If they seem to bother him, try Benadryl (call your vet for your dog's dosage and to confirm it is safe for him). If they persist, get a professional opinion.
I agree with KAL - it sounds like an allergic reaction to something, possibly insect bites. For otherwise healthy dogs, the dose of benedryl is 1 mg per pound of the dog's body weight. Hope your pup is doing better by now. :-)
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