Is the GRO reference the same? If so, it is not a duplicate registration, just a duplicate index entry. If not, and the second was some time after the birth, it is probably a reregistration following the parents’ marriage
You don’t say when the birth occurred, but it is worth remembering that before 1969 no surname for the child was recorded on the certificate. The surname(s) appearing in the GRO index are extrapolated from the information recorded about the child’s parentage.