Mortgage Interest Relief is calculated on the interest charged/paid on your mortgage for a given year. Because you have paid off some extra capital outstanding on your loan during that year, the interest that you are being charged by your lender has reduced & differs from what they would have estimated to Revenue in respect of your mortgage interest for that year, therefore your interest relief has been adjusted to reflect this.
You have not been penalised, as the extra amount that you paid has reduced the capital amount owed to your lender, so you will not be paying interest on this amount at all (so you are not missing out on any interest relief), unless there are any penalty charges/fees to take into account under the terms & conditions of your loan agreement.
Interest relief reduces anyway over the seven years, but Revenue wouldn’t under normal circumstances write to you to inform you of this.
Basically you won’t get interest relief for interest that you did not pay.