Overpaying AVC's, some not covered by Tax Relief

Company I work for has a pension scheme in place for which they first make a contribution on our behalf of 6% salary and then allow us to make additional contributions (AVC's) up to 9%, for which they match.

I'm thirty now, but only just realised that as I have been making a AVC of 6%, this puts the total pension contribution of 18%, which is 3% over the Tax relief limit for someone in their twenties (Tax relief limit is 15%).

I'm currently looking into submitting tax returns to get money back on medical expenses and wondering if I should be looking to make this right, or I'm not 100% if I need to do anything with respect to the tax on the additional contributions.

Question on how this works:
1. Tax relief seems to be applied at source by employer, is onus on employer to do the calculations so I pay tax on the 3% as part of monthly salary i.e. for them not to grant me tax relief?
2. When filing a tax return should I be declaring this 3% (in some way) as needing tax to be paid on? Or will this automatically get calculated by Revenue, in that they'll recognise that in 2017 I claimed tax relief on pensions of 18% and not the allowed 15% and they will subtract what is owed from the claims for medical receipts?