Confusion about marriage records

yes - Hattie/Hettee or Hester are alternate versions of Esther, but the two parishes are in different locations, and not adjacent - so I think two separate marriages of people who happen to have the same names, or less likely one couple married twice, or possibly a mixup in locations. Maybe a look at the register images when they become available online might help solve this..

Are there any other details on the transcripts that might help, e.g. are witnesses the same, are any places of residence given, or name of the priest ?

EDIT : I suspect that the Ancestry record may have been misclassified, and listed under the wrong parish. I've seen this before with other parishes, but they dont have register images for this marriage so difficult to confirm.

The 'duplicate' Offaly/Westmeath records on RootsIreland are probably  due to the fact the the RC parish of Kilbeggan is very close to Co. Offaly and may have covered parts of that county - The date is probably unclear in the original, or assumed based on other records and that's accounts for the small difference.

I would trust the RootsIreland transcripts on the classification of these. Even though all the records are on one website, the records are provided by a Federation of county centres, and I doubt one of these would transcribe the records of an incorrect parish, not local to themselves from a different county by mistake.

You can often confirm the details by parish by scrolling back to the beginning of a register, either on film or online, and check to see if introduction notes mention details of the parish. There can also be details of the parish priest and curates mentioned, either at the start of a register or when a new priest takes over etc.. Priests can often be traced in directories to confirm where they were based.

It may not be possible on thier system, but a search through the transcripts on Ancestry of the marriage records for 'Kilcloon, Batterstown and Kilcock' might locate a record with a clue to help solve this - e.g. a place of residence that proven to be in Westmeath/Offaly or Meath/Kildare, or the name of the parish priest, or maybe something like a very distinctive witness name ?

The parish names sometimes have variations, which I think may have lead to the mixup. e.g. a parish can go by the names of one or more of the civil parishes it covers, a town or village name(s) where a chapel is located, or even a place name were a chapel was previously located.

Did your Bernard and Ester/Hettie have any children born/baptised in the same area ?

I suppose they could be mixing up the Diocese of Meath and the County of Meath. The name they list for the parish is distinctive and definitely on the border of County Meath and Co. Kildare, and not close to Kilbeggan, which is over 60km (~40 miles) to the the west.

By coincidence there was another post here today that mentioned a marriage listed in the same parish of 'Kilcloon, Batterstown and Kilcock' which was again located on RootsIreland in a different parish miles to the west in Co. Offaly, so I'm even more certain there's some sort of mixup going on.....

I had a quick look through the 'Kilcloon, Batterstown and Kilcock' marriages on Ancestry earlier and the details seem a little abbreviated, i.e. I didn't see any space for remarks, addresses or priest names etc. There are a number of possible leads to Offaly and Westmeath rather than Kildare/Meath, but the most certain clue was a slightly more recent marriage which I was able to cross-match using extracted civil records as having taken place in Clara, Co. Offaly, (in yet another parish) again miles away from Kilcock and Batterstown - and this like your marriage for Bernard and Esther matched date, the full names of the bride and groom etc. It may be complete coincidence - the town of Clara, like Kilbeggan, is also near the Offaly/Westmeath border ..

Without images of registers, including cover pages, notes etc it may be difficult to prove 100%, but the now at least three seperate marriage matches, all listed under 'Kilcloon, Batterstown and Kilcock', to corresponding records in separate parishes on RootsIreland doesn't make any sense, unless these Kilcloon, Batterstown etc records are classified or indexed incorrectly, so I think I'd stick with RootsIreland opinion on these, and list your marriage for Bernard and Esther under Kibeggan RC parish, Co. Westmeath.

(The 'duplicates' on RootsIreland are understandable, as the parishes cover parts of more than one county, so the records are listed under each county centre)

EDIT : I've sent a question on this to Ancestry, although I suspect they only have transcripts, so might not have any way to provide a definite answer.

I've had replies to my query from both Ancestry and RootsIreland - I'm not at all convinced by the one from Ancestry, all they say is that the records originated from Parish Registers Parish which are located in the National Library of Ireland. 

Irish Family History Foundation / RootsIreland gave more details and mentioned that this was pointed out back on 2011 when these records were released by Ancestry. They also gave a link to sereval comments posted at the time,  including one that by a respected Genealogist who came up with evidence re the mis-classification of records - see here