I came across this thread while browsing and note that there are a couple of knowledgeable people who have contributed. May I please ask a question regarding the NLI Wexford Catholic Registers?
I have searched unsuccessfully in the registers for a baptism of an ancestor in about 1863, said to have been born in New Ross. The odd thing is that I can not even find one other baptism with the same surname (and it is generally common to see surname patterns when you look through old registers). I have the same issue with a baptism in about 1864 in Wexford.
(I did search for several years after these dates)
Does anyone know if there are missing entries for this time period in New Ross, and Wexford? The dates appear to have been digitised, but I am wondering why neither of my ancestors appear in either New Ross or Wexford where they say they were born. Can anyone offer any explanations or assistance please? 
I apologise for hijacking your thread M.
Well, I can offer a specific suggestion, and some general comments.
The specific suggestion is that that part of New Ross lying across the river Barrow, on the Kilkenny side, is actually part of the Parish of Rossbercon (or Tullagher as the NLI seem to name it for some strange reason). So, you should probably check there too.
The general comments are:
1) Simply a case of omission or error. The omission rate, even in well kept registers, was frighteningly high. I have two great-uncles/aunts whose baptisms in the 1880s are simply not there, anywhere. In earlier generations I have many, many more "missing", who "should be" there, including in 1860's Wexford.
2) Ages on later records are commonly 10-15 years off, usually on the low side. So, you really have to check up to 10-15 years BEFORE dates of birth estimated from census or death records (even 20 years in extreme cases), not so much after.
3) It sometimes happened that a child might be born in one location, and baptized in another (rare ?).
4) That your relatives were mistaken or mis-recorded where they were born. I have seen multiple instances over the years where a stated place of birth is not in fact where I know they were actually born. e.g. not unusual for child to be born at maternal grandparents house, etc.
5) Exotic possibilities exist. I spent 20 years searching for the birth of a supposed relative, Sarah Roche, born ca 1878. Searched the whole country several times over, and all of England as well. Simply could not find her. Discovered a year ago from a will that she was actually adopted! (So never will discover her birth identity).
So, I am afraid that everything is possible, and in my personal experience, all the above happened! That said, options 1) and 2) above are by far the most likely.