For starters, on most (all?) FHA loans you have 0.25% APR tolerance. You get double the normal tolerance because the monthly payments drop every year (due to the decreasing MI renewal premium.) These annual steps in the payment schedule meet Section 1026.22(a)(3)'s definition of an "irregular transaction." Detailed explanation is here
You are correct to conclude that there is a FC violation but no APR violation. Corrective action comes in two flavors.
If your regulator discovers FC understatements during a compliance exam, you will be ordered to search your files for all similarly affected borrowers and follow the interagency enforcement policy regarding reimbursement. That policy allows you to apply "cross tolerances." In your case, that means you would convert the unused portion of the APR tolerance (0.25% - 0.055 = 0.195%) to a dollar equivalent and use that number as the FC tolerance for reimbursement purposes. That value will very likely be MUCH higher than the $100 Reg. Z tolerance. Comparing your understatement with this cross tolerance, you will probably be off the hook--no reimbursement required. (APRWIN does all the math.)
Flavor #2 is self-discovery. When you discover the FC violation without your regulator's help, you have the option
to cure the violation. The cure procedure is spelled out in Section 130(b) of the TILA. Part of the cure will be reimbursement of any understatement outside Reg. Z's tolerances--no cross tolerance recognized.
If you decide to take the cure, think carefully about keeping the $100 tolerance. If the borrower should ask how the amount was determined, you will have to admit that you chose to screw him/her out of the first $100 of YOUR ERROR!