This happens more than it should, and you can usually get the mail fee removed if the plate was linked at the time of the trip. I had a similar issue on the RFK years ago, and the same rule applied.
First thing I do is check the transaction time and plate on the Tolls by Mail notice against the E-ZPass account. If the plate is active and the card on file was valid, the likely culprits are a dying transponder or a windshield position issue with the newer tags.
Call the E-ZPass service center, not the Tolls by Mail number first, and have the notice number ready. Ask them to convert the toll to your E-ZPass account and remove the administrative/mail fee as a courtesy. Important caveat: if the plate was added after the crossing, they usually won’t waive it.
Also dispute it before the due date if possible. Once a Tolls by Mail bill moves toward collections or becomes booting-eligible, the conversation changes completely. If the transponder is older, ask for a replacement; they’ll sometimes handle that in the same call.
Don’t assume paying the bill means you’ve admitted fault. You can still ask for a refund of the extra fee after the fact, but it’s much easier to get them to zero it before you pay. I’d also screenshot your E-ZPass account showing the plate and tag ID active as of the crossing date.
