The spelling issue would be due to whoever wrote down the record, as you suggest. As you don't say what period you're looking at, or what kind of people they were, it's difficult to say whether they would have been able to write. My lot couldn't write before around 1830. The parish records would show you their signature or mark, if you have a look at the originals or the microfilm. Failing that, I'm sure there's a local history group who might be able to help you.
I would suggest that you go back another generation or two, if possible. It's well within the realms of possiblity that there was more than one William Skaife, if William was a popular name in the family; they could be cousins, for instance. Jane is hardly an unusual forename, either. If you find two marriage entries for William Skaife with a Jane Somebodyorother, then you're on the right lines. I just did a two-second search on the IGI and found all these Williams who married Janes, somewhere in Yorkshire:
International Genealogical Index / British Isles - 9
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1. WILLIAM SCAFE - International Genealogical Index
Gender: Male Marriage: 17 SEP 1829 Marske By Richmond, Yorkshire, England
2. William Scaife - International Genealogical Index
Gender: Male Banns: 29 JUN 1761
3. WILLIAM SCAIFE - International Genealogical Index
Gender: Male Marriage: 29 JUN 1761 Hampsthwaite, Yorkshire, England
4. WILL. SCAFE - International Genealogical Index
Gender: Male Marriage: 30 JUN 1733 Garsdale, Yorkshire, England
5. WILLIAM SCAFE - International Genealogical Index
Gender: Male Marriage: 18 MAY 1778 Saint Mary Castlegate, York, Yorkshire, England
6. WILLIAM SCAIFE - International Genealogical Index
Gender: Male Marriage: 31 DEC 1830 All Saints Pavement And Saint Peter The Little, York, Yorkshire, England
7. WILLIAM SCAFE - International Genealogical Index
Gender: Male Marriage: 28 NOV 1732 Hawnby, Yorkshire, England
8. William Scaife - International Genealogical Index
Gender: Male Banns: 29 JUN 1761 Hampsthwaite, Yorkshire, England
9. WILLIAM SKAIFE - International Genealogical Index
Gender: Male Marriage: 26 NOV 1817 Kirby Wiske, Yorkshire, England
That's 7 different marriages. I don't know what period you're looking at, but the 1829 and 1830 ones could cause some confusion. Number 6 could easily be the grandson of Number 5, and the cousin of number 1, given that they would have been married close to the bride's family.
Failing that, look at when the children were born. In my family they tended to pop them out every two years or so, so 16 children without twins indicates a very long period of fertility
