Welcome to the Wefugees Community and thank you for sharing your situation with us.
I was trying to make some research, but unfortunately the found information can not give a clear answer to your issue. Maybe those complications are related to the fact that eventually your residence permit will depend on the declaration of the fatherhood and the immigration office (Ausländerbehörde) wants an official authority to look at your case. But this is only a guessing. Another assumption: The (identity) documents you showed to notary were not "sufficient".
It could be the easiest and smoothest way to explain the "Jugendamt" the immigration office's response. Provided that they can offer you a respective appointment in the near future.
I will link one of our experts here. Dear @alla_fka, can you give us more information on this?
In any case, seeing a (migration) counselling office can be also helpful! Let us know if you need support in finding one in your area!
All the best,