The good news is, I suspect your Medicare claims will continue to be paid as it's highly unlikely that CMS is using a third party data aggregator to scrub claims.
It's not unusual to see issues with data aggregators, and in the fine print you'll often see mention of an error rate. We use several different aggregators (LexisNexis is one) when performing investigations & correlation studies on possible matches. Where we benefit from having time to evaluate/escalate/reason whether the data being returned is reliable, the prescribing/ordering/referring provider scrubbers rely on fast computer-only driven insights – with accuracy being a tradeoff.
With that being said, I do wonder whether your party's NPI could be associated with another excluded provider (perhaps with a different name). These scrubbers are usually driven by NPI as it's a standardized and unique identifier (unlike a name search). If you'd like to contact me offline with the name and NPI in question, I'd be happy to check our databases for clues. If this suspicion is true, I'd bring the issue to the agency in question to correct their data. If the NPI is clear and the pharmacies can't override/release the order from their scrubber (I suspect they can, but might not know how), I'd probably escalate to their compliance office. If that doesn't work, or perhaps in tandem, you can also try to find out what program(s) these pharmacies are using to scrub the ordering/prescribing docs and contact the software platform's compliance department.