I have worked for an insurance company before, processing claims. It is feasible that it could very well be a duplication issue. Many Medicare Participants also have addtional coverage, to cover some if not all of the difference that Medicare does not pay. If a claim is submitted by the provider, AND the participant, and even perhaps the Third Party payor, that would result in a duplicate claim and then a denial.
Additionally, putting my processing hat back on, I remember the common mindset was to pay claims, without doing any reasearch on whether or not it should be paid. The thinking behind that was if you paid a claim there would not be any call back from anyone complaining, therefore you wouldn't get in trouble. Audits were usually 10 claims out of 100, so you could still pay some correctly, and not get caught for over paying. Now, with that being said, most insurance companies have automated the process of paying claims, and more than likely the computers are paying only those they should.