Discrepancies do happen because of some irresponsible people running the office. With your problem, you have no choice but to fix it legally. Go to the local civil registrar from where your son was registered. You can apply for correction of entries. There are several forms you need to fill out and several documentary requirements you need to submit. These documentary requirements will be used by the office to estaablish your relationship with your son.After compliance you will be scheduled for a hearing normally by the officer of the local civil registrar to validate your entires, be sure to answer it the way you filled out the forms.They would check consistency.After that the office would endorse it to the National Statisitcs Office after their office made the corrections. You will be told when to apply for an NSO copy on security paper, then you can now apply for the passport of your son. Do things one at a time and do it legally because if not you will end up having more legal problems in the future.