Were both the first registrations done within 6 weeks of you being born? This is the statutory requirement. If one was done outside this time, then I'm not sure what would have been happening.
If both were actually done within the six weeks, then I would suggest that perhaps the registration was done in error by two different people not knowing the other had already done it. The person registering in the maiden name could have done so knowing the divorce was happening but not realising that it hadn't actually gone through yet. Perhaps your mother was actually using her maiden name again but legally still with the married name - the person doing the duplicate registration may not have known this.
I think if there is an attempt to register the same child twice (in New Zealand where the registry offices wouldn't be dealing with the numbers of events that UK offices would) it would possibly be picked up if the surnames were the same, but much less likely if two registrations have been done in different names. It would be interesting to see both certificates and see who the informant was in each case.