Good find Annette.
I would try the GRO again without using the reference for the surname MorganS, year of birth 1859, place of birth St Dogmells, parents John & Maria MorganS and see what happens this time. It does take about 15 working days to process these orders, with a reference takes up to 5 working days. If there's no match again you'll get your money back.
If the reg office do make this charge (and it's not the only one), it would be a last resort. But if the GRO don't find the 2nd application, there may not be a cert to find, as I mentioned before, and you may not get all your money back from the reg office.