That's actually pretty common. Maybe they just didn't want to marry one another?
There was of course a stigma attached to illegitimacy, but in some areas it was so common that it was an everyday matter. It's quite usual to find in mid-19th century censuses a couple in their 50s or 60s or even 70s with a string of young grandchildren, all with different surnames.
The authorities in Banffshire were astonished when they looked at the records of the first year of statutory registration of births. They found that 19% of the babies registered were illegitimate. The illegitimacy rate varies enormously from one part of the country to another - in some areas it was just 2%.
Illegitimate children were often known by their father's name, even if his name was not on the birth certificate. Sometimes they changed their surnames, being know at one time by their father's surname and at another time by their mother's. Or they might appear in records with both surnames. The important thing to realise is that there were no hard and fast rules about this.
The father's name can only be on the birth certificate of an illegitimate child if he accompanies the mother to the Registrar's when she goes to register the birth, and he signs the register then and there. It cannot be added later to a birth certificate.
So it's perfectly possible that an entire parish knew who the father of a child was, even though his name never appears in any formal record.
However there are two ways of the name of the father of an illegitimate child getting into the statutory birth records even though it isn't on the birth certificate, and never will be.
If the mother goes to court and gets a paternity order against the father, the Register of Corrected Entries (RCE) will contain that information, and the original certificate will be annotated with a reference to the RCE.
If the parents subsequently marry, that legitimises the child provided that the parents would have been free to marry at the time when the child was conceived. In these cases, the birth is sometimes re-registered many years later with the names of both parents. (A child of an adulterous liaison is not automatically legitimised if the parents marry at a later date.)