Female converts will also have another name: xxx bat Sarah imenu (xxx daughter of Sarah our mother). It's not surprising. Jewish women have two names: xxx bat [name of the father] and xxx bat [name of the mother].
A man who would be called xxx ben [name of the mother] would be the son of a Jewish man who converted to another religion or a bastard. It also happened a couple of times in North Africa, when the parents were divorced and the son clearly sided with the mother.