The PBM Sent Back a Discrepancy List. Here’s Why Everything Just Got Harder.

Mark Boesen, PharmD, JD, is a licensed pharmacist and attorney and a founding partner of Boesen & Snow Law, with over three decades of experience in pharmacy operations, healthcare law, and public policy.

Mark K. Ziegler, Pharm.D., M.B.A., is Director of Payor Compliance & Credentialing at Boesen & Snow Law and a former PBM Audit Team Leader.

In the last piece, we walked through the audit notice and the first submission. If you did that part well, you’d think the hard part was behind you. It usually isn’t. Almost every audit (even a clean one) comes back with some kind of discrepancy list. That’s where a lot of pharmacies get their first real shock: a dollar figure attached to their name that feels like it came out of nowhere.

It didn’t come out of nowhere. It came from a gap between what was sent and what was actually required. The difference now: that gap has a price tag on it, and closing it just got more complex.

What Actually Shows Up in a Discrepancy List

Once the PBM reviews your initial submission, you’ll get some version of a list: the specific claims it considers unsupported, a preliminary dollar amount, and a new, more detailed round of document requests. That second round is what catches pharmacies off guard.

Think of it as a goalpost shift. Whatever level of proof got you through the first submission is no longer good enough for the same claim at this stage. A single missing detail on an otherwise solid document doesn’t just get flagged and waved through with a note. It gets rejected outright, and what replaces it is almost always bigger than what came before.

Here’s how that plays out on an actual claim. A pharmacy collected a copay by credit card and submitted the receipt to support it, the same kind of gap we described in the first article, just further down the line. The receipt shows the right dollar amount, the right date, the last four digits of the card, and the authorization number proving the charge went through. Everything checks out except one thing: the prescription number for that fill was never itemized on the receipt. That’s it. One missing line item. Because that detail is missing, the PBM won’t accept it, and the claim comes back as a discrepancy.

Fixing it now takes a lot more than reprinting a receipt. The pharmacy needs a signed attestation from the patient confirming they paid that amount, on that date, for that specific prescription. In many cases, you’ll also need to go back to your credit card processor and pull a merchant report proving the payment was actually received. What started as one document is now three, and that’s the simple version. On more complicated claims, one missing piece of documentation can turn into four or five separate items to track down, each one harder to get than the last. A patient attestation is the hardest: the patient may not remember the transaction, may have moved, or may simply not respond. Multiply that across every claim on a typical discrepancy list, and a pharmacy that started with a single stack of receipts is suddenly looking at a mountain of paperwork. Some PBMs will contact prescribers directly to ask whether they actually wrote a given prescription, and a doctor who was just declining to authorize a refill can answer in a way that reads as a denial of ever writing it at all. Others survey patients directly, and a patient who genuinely doesn’t remember paying anything close to the original copay, because a coupon brought it down, can unintentionally create what looks like a denied claim. None of this means fraud occurred. It means the paperwork required to prove otherwise just multiplied.

Consequences Don’t Wait for a Final Ruling

A PBM does not need a final determination to start acting on a preliminary number. This isn’t the PBM improvising: what it can do at this stage, including withholding payment before anything is finalized, is generally spelled out in your own provider contract and manual. It’s a term you already agreed to, which is exactly why it’s worth knowing before you’re staring at it in a letter. If the discrepancy amount is large enough, some PBMs will begin withholding payment on new claims immediately, collecting against that balance while the pharmacy is still contractually required to keep filling prescriptions. You keep working. You just stop getting paid for it. Letters at this stage will also frequently include termination language, framed as a possibility rather than a decision; it lands hard regardless. None of that means the outcome is decided. It does mean this stage deserves the same seriousness as the original audit notice, not less.

The First Real Chance to Push Back

Once the discrepancy list arrives, the pharmacy typically has a defined window, often around 30 days, to respond with a formal appeal. This is the real second shot: new documentation, corrections, and direct pushback on findings that don’t hold up.

Not everything is worth fighting, and knowing the difference matters. Take a straightforward billing error: the prescription authorized a thirty-day supply, and the pharmacy dispensed and billed for ninety. There’s no attestation, no screenshot, no additional record that changes what was billed against what was authorized. The finding is what it is. Spend your limited time elsewhere. Save the fight for findings where evidence exists or can still be gathered.

Time management matters even more here than at the notice stage. We talked last time about blocking out real time on the calendar instead of treating a deadline as a single due date. At this stage, that habit isn’t optional. A signed patient attestation doesn’t materialize because you asked for it once. It takes a phone call, sometimes several, sometimes a mailed form and a wait for it to come back signed. A merchant report has to be requested from your credit card processor and followed up when it doesn’t show up the first time. None of that happens in a spare ten minutes between patients. It happens because someone blocked out real time specifically to chase it down.

A strong appeal is not a stack of documents dropped into an envelope. It’s an organized package, typically a formal letter with every piece of supporting documentation attached as a labeled exhibit, so a reviewer can follow the logic without having to reconstruct it themselves. How something is explained matters almost as much as what’s attached. A short, factual explanation next to the evidence lands better than the same evidence with no context around it.

That said, there’s a real difference between a plain operational explanation and a legal argument, and pharmacies tend not to know which one they’re dealing with. We’ve seen cases where a pharmacy had a completely legitimate shared services arrangement (one location handling data entry, another handling dispensing) and in trying to explain it themselves, described it in a way that sounded like exactly the kind of arrangement the manual prohibits. Nothing about the setup was wrong. The explanation was. Pharmacies generally believe they’re in the right, and in making their case, volunteer detail that wasn’t asked for, which raises new questions instead of resolving the original one. What gets left out of an appeal often matters as much as what gets put in.

Where This Leaves You

Everything at this stage traces back to the same lesson from the first submission, just at a higher cost. A gap that was simple to close with the right document early on becomes complex to close later, once it requires attestations, merchant reports, and prescriber statements instead. The paperwork doesn’t grow in a straight line. It grows exponentially, one missing detail at a time, until what should have been simple turns genuinely complex.

We’ve handled hundreds of these audits across every major PBM, and we know which fights are worth having and which aren’t. Generally speaking the earlier we’re brought in, the more of that gap we can close before it turns into a signed check. If your pharmacy just received a discrepancy list, bring us in before the appeal window closes, not after.

Next in this series: what happens when the PBM issues its final findings, and the narrow window most pharmacies don’t know they still have to fight back.

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Boesen & Snow Law is based in Scottsdale, Arizona. We work with independent, specialty, and multi-location pharmacies nationwide on PBM audit, network, and compliance matters. Our ability to formally represent a pharmacy in a particular matter, including in litigation, arbitration, or before a state board, depends on that jurisdiction’s licensure and admission requirements, which may include pro hac vice admission or association with local counsel. Contact us to confirm we can assist with your pharmacy’s specific state and matter.