Thank you for reaching out to the Wefugees community.
With the student visa you can only work 120 days full-time or 240 days half-time. So, that is may be the reason why your boss didn't accept your visa.
For the resident permit as a father of a german child you need "Sorgerechtserklärung" and "Vaterschaftsanerkennung" Do you pay child support?
If your papers are ok, there should not be a problem with your resident permit. I wish you the best.
I hope my answers were helpful and I would be very happy if you would contact me again with further questions. I'm a member of the mbeon-staff and I‘ll be glad to help you over a longer period of time. mbeon is an online advice for migrants via the mbeon app, which you can install on your smartphone for free. Download it from App Store or Google Play Store. You’ll find me in the mbeon-app under my location Mannheim and then my name Frau Schünemann and get confidential one-to-one advice in a safe virtual room where nobody can read messages. For Further information please visit www.mbeon.de.
your mbeon advisor