Don't know if this is of use to you since you didn't say where your gf lived.
I have the same thing with my gm's family from Krakow. She had 2 brothers and a sister. Two of each had their mother's surname and others had their father's. On their marriage banns records there is a note "surname of the unregistered father."
The Austrian-Hungarian empire only recognized marriages done by the Catholic church. All other marriages were illegitimate. However, by the time my uncles and aunt were married (1907-1914). This rule had been changed. My grandmother was already in the US and married there.
I never got a good answer for why this was still happening. But I haven't asked about it in ages.