Interestingly, the IGI at
www.familysearch.org does not list an Isabella McInnes, daughter of any McInnes and Isabella Orr. It does list Isabella McGinnis, born 3 October 1870, daughter of William McGinnis and Isabella Orr, as well as William McGinnis, 1864; Francis Orr McGinnis, born 1868; and John Boyle McGinnis, 1873.
(If you are calculating a date of birth by subtracting an age in a census from the census year, you will get the wrong answer three times out of four because the census was taken three months into the year, when only about one person in four had actually had that year's birthday. Someone born between early April 1870 and December 1870 would only have had their 30th birthday, not their 31st, by the date of the 1901 census)
So, why might Isabella have got her father's given name wrong?
There's a family at 20 Barony Street, Glasgow in the 1881 census consisting of Isabella McInnes, head, 36, widowed, with son William, 16, bottle blower (matching a birth date in 1864/5); daughter Isabella, 10 (matching a birth date in 1870/1); son James Clark McInnes, 3; and sister Barbara Orr, 33. I don't think there is much doubt that this is your Isabella Orr with her surviving children.
Now, when did her husband die? The IGI doesn't go beyond about 1874, so young James isn't listed. But look at his middle name, and look at Isabella Sr's name as shown on her daughter's marriage and death certificates. Why would William McInnes or McGinnis give his son the name of his future widow's future husband? Could it be that James is in fact an illegitimate son of Isabella Orr or McInnes/McGinnis, born after the death of her husband?
So, if we assume that William was alive in 1872 when John Boyle McGinnis was conceived, and had died before, at the latest, 1877, when James Clark McInnes was conceived, we have a fairly short window during which William could have died. Also, we can assume that William was aged at least 20, and it seems likely that he died in Glasgow. Using those parameters in SP gives us seven possibilities, but one can be discounted as too old (68) and one is just 20, so probably too young. Just one of them spells his name McGinnis, and bingo! It is the right one. William McGinnis, bottle blower, married to Isabella Orr, died 12 July 1875 in Barnhill Poorhouse.
So he died when his daughter Isabella was not yet five years old. She would barely have remembered him, so it is not surprising that she got his name wrong fourteen years later when she married.
Now, why did she think his name was James? Note again the given names of her brother James. It is quite common for the mother of an illegitimate child to name her child after its father. There is a marriage in 1883 of an Isabella M*inn*s to a James Clarke in Glasgow. Substituting Orr for M*inn*s produces the same result. So I think that Isabella had an illegitimate child, James, to James Clark(e) in 1877/8, and then married the father in 1883. So James Clark(e) had been around since Isabella was six or seven years old, and it was his given name that she supplied on her marriage certificate.
So if I am right, for once the information on the marriage certificate is wrong and the death certificate is correct.
As an aside, note that William died in the poorhouse. This suggests that there may be something about him in the Glasgow Parochial Board records (Poor Law/Parish Relief records) which are in the Mitchell Library in Glasgow. If so, they will contain a wealth of information abour William.
(With a surname like McGinnis, and his children's given names including Francis and Boyle, it would not surprise me at all if William was Irish; if he was, and if there are parochial board records of him, they are quite likely to tell you where in Ireland he came from.)
So many ifs, buts and maybes. You need to get the birth certificates of Isabella jr and her brothers; these will tell you when and where William and Isabella Orr were married (this information is not in the IGI). The Clarke to Orr/M*inn*s mariage certificate will confirm or otherwise the identity of Isabella Orr's second husband, and will provide the names of her parents. The birth certificate of James Clark(e) or M*inn*s in 1877/8 may also be informative. Was Isabella Orr deceased by the time her daughter married in 1889? This would narrow the search for a death certificate.