Looking now at the names and dates you have mentioned. I wouldnt recommend relying on IGI as being totally accurate. If the source information includes the word "REGISTER", I think that is good quality record.
You have the marriage certificate for James BERTIE in 1856. That will give his parents' names, hopefully.
Not being able to find him in a census is not unusual. I've found a number of mine with their grand parents, or even working. They worked from as young as 13 yrs or even younger.
In addition to Margaret's siblings you have, there's a Marjory Collie BERTIE b 22.5.1865 Montrose and James BERTIE b 2.11.1868
Don't think the name SKENE is that common but someone will always come up with surprising evidence in those circumstances. I wouldnt necessarily take the age in 1841 as being too accurate. Check out a later census and of course a certificate.
Hope that what I have said is helpful though I am not sure you were replying to me in the first place.
Certificate information can be inaccurate but its better than IGI or Ancestry.
I did find a grieving husband didnt know the correct names of his wife's parents, but maybe thats forgiveable. I found him listed as an Informant in the village and that could be worrying as he's known to have been a colourful character!
Hope theses musings help.
I have James BERTIE, son of James and Helen SKENE b 1 August 1831, married 29 February 1856 to Mary Ann ALLAN b abt 1834. I have Elizabeth BERTIE b 9.9.1863 as a daughter of James and Mary Ann ALLAN