Two registrations, or do they appear in the index twice? Since their parents were not married, you may be seeing the entries appearing under both surnames. I'm not sure at what point the birth certificates started a separate field for "surname of baby" but historically the baby did not have a separate surname and surname was assumed from the name of the parents. In the case of an unmarried couple who both were named on the certificate, you would see the same entry for the baby but written under both his surname and her surname (check the GRO number- if it is the same, we are talking about the same entry).
The middle child might have been an occasion when the father could not attend the registration so his name was omitted from the birth certificate? In which case the birth would be indexed only once- under the mother's surname.
Does that line up?
The other possibility, although I think the year of registration would be altered here, is that the children were legitimised after the marriage and the births amended accordingly. Not sure why not the second one though.
