I have both transcriptions and certificates for the marriage, there are even two volume numbers for the marriage very odd.
It is not at all odd to find more than one entry for a baptism or a burial or a marriage in the era BEFORE civil registration commences.
Back in Sept 1810, Gov Lachlan Macquarie issued a general order regarding the recording of baptisms and burials, (later extended to marriages). So that the clergy (of the various denominations) were expected to not just record a baptism or a burial in accordance with their own denomination's Church Laws and Practices, but also to transmit a summary (each quarter) to the NSW Chaplains. So, say a person (any age, baby to adult) was baptised anywhere within the then territory of N S Wales.... the clergyman would record it in his own register .... and then transmit that to his own denomination's Head Office in accordance with his own Church laws. But on top of that, he was under civil general orders to also transmit a summary to the NSW Chaplains. This general order and the practices it developed, continued to operate (more by breach than observance) until the commencement of civil registration.
When the NSW BDM commenced, then many of those Early Church Records came across to the NSW Registrar General's office. They were NOT put into Volumes until around 1912 and they were not indexed until around 1930. And the NSW BDM has not ever claimed to hold ALL the records.
http://www.records.nsw.gov.au/state-archives/guides-and-finding-aids/short-guide-2/short-guide-2 (click on the various headings .... baptisms, burials, marriages)
http://www.records.nsw.gov.au/state-archives/guides-and-finding-aids/short-guide-4/short-guide-4 (scroll through and click on many headings there too)
And
There were TWO marriages listed at family search for a William BROWN and a Matilda WATSON .... two different dates .... do you definitely have BOTH those records? two different volumes at NSW BDM so may I please ask which one matches up to which family search record please....
Cheers, JM