Your ancestor may have had no idea of the "right" way to spell his last name. Correct spellings are a somewhat recent affectation for a variety of modern reasons. Even your literate ancestor may have been inconsistent in spelling his name--if the name "sounded" like his name it was his.
As a relative of mine once said (paraphrasing) "If doesn't matter if my wife calls me Janssen or Johnson. When it's time for supper ,I'll come in to eat no matter which name she uses."