The fee is not a medical expense but it is neither a distribution taxable to the recipient.
You go on to state "
I have received a 1099-SA with distributions totaling those fees"
The advice is the custodian has filled out the 1099-SA wrong and reported those to the IRS as distributions. The custodian needs to provide a corrected 1099-SA.
You have to followup with the custodian.
If the custodian refuses to correct the 1099-SA get that information in writing from then and you would need to retain the supporting documentation that they are refusing to correct the 1099-SA.. You could then paper file using your corrected distribution amount(amount not including the fees) and include a letter of explanation why your box 1 reporting to IRS is different from the custodians. Clearly state that the distributions were fees taken directly by the custodian and were not distributions made directly to you the recipient, (Account statements would support those were taken as fees and not distributions) and are expenses not to be reported in box 1 of form 1099-SA as distributions.
