A double problem

As I move on from the M'Ilhagga indexes in Ancestry.co.uk to McIlhagga I find there are two sources for births, first 'Ireland, Births and Baptisms 1620-1911', and second 'Ireland, Civil Registrations Birth Index, 1864-1958'. I have immediately hit a problem. The oldest name in both sources appears to be the same, John 1865, born Connor, Registered Antrim.The first Index tells me the father is John and the mother is Eliza McCullough. In fact I have a double problem. For this couple I already have a son William G. born on 30 Jan 1865 (the Index gives me John born 31 Jan 1865), and I also have a John born September 1868. Were there two Eliza McCulloughs who married two John McIlhaggas about the same time, who both had a son John? Eliza's surname does get spelled two slightly different ways, McCulloch and McCullough. What the second index tells me is that there were certainly two Johns born, one in 1865 and one in 1868, both registered in Antrim District. (The second source doesn't give parents' names). One possibility is that the first John was a twin of William G and died, and that he was 'replaced' by a John born three years later! I suppose light will dawn at some stage.