Dear @Lili,
Welcome to the Wefugees Community and thank you for reaching out to us.
I checked the section of the German Residence Act you mentioned and I actually doubt that this one is connected to the "GüB" (Grenzübertrittsbescheinigung) or any potential entry ban.
As far as I see the situation, your daughter most probably was not issued a re-entry ban to the EU/Schengen area. If she left Germany when the immigration office asked her to do so and she submitted the GüB at the border (or proved in another way that she left Germany within the required timeframe), she may apply for a new visa whenever she wants. The non-extension of the residence permit and the subsequent request to leave the country is not an issue filed in any criminal record. Don't worry!
Do you agree dear @mbeon-Christine or @mbeon-fardeen and is there anything you would like to add?
In any case, please also don't hesitate to get back to us with any further questions.
All the best,
Meike