I'm an international medical student in Germany. 6 months ago I got married to my girlfriend. She decided to get a visa to visit me, so she applied for a Schengen visa from the Spanish embassy in Bahrain. She got a visa for 6 months. It is valid from 04/04/2018 to 30/09/2018.
She came to Europe twice: the first entry was in Barcelona on 17/04 and exit was from Düsseldorf airport 09/06. She stayed in Europe for 53 days.
The second visit was in Düsseldorf from 28/06 to 23/08: 56 days. She is still here in Germany with me.
On the second visit she took one German course, as she plans to apply here for work or study in the future. So for the two visits she stayed here more than 90 days, around 110 days for 2 visits and the visa ends on 30/09.
What should I do? What is the best airport to exit from? Cologne-Bonn, Düsseldorf in Germany, or from Belgium, Spain or another country? Or should I try to change the visa type here in Germany?
Will she will get a ban or fine when she exits the Schengen area? If she applies for a new Schengen or study visa later, will it be OK?