This is not a regulatory issue, it is a matter of breach of contract. There are no regulatory restitution requirements in Regulation DD, nor are there any civil penalties associated with violations of Regulation DD (they were repealed).
If you want to "do the right thing", do it in the most cost effective manner available to the institution. I would think that a credit to their monthly statement and a statement message would probably foot the bill. If you try anything else, checks and letters, based on what you said the adjustments would be, the administrative costs are going to far outstrip the corrections (stationary, postage, etc.).
Depending on the amount of time over which this error happend - less than $.10 per account may simply be chalked up to nothing more than a rounding error.
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