She might get in trouble on her final way back home when she leaves the Schengen area. European and Schengen countries have out-going passport controls and they check passports and visas. While I doubt that she will face any serious consquences she has to be preapred that the border officer will ask her some questions why she stayed longer than 90 days. In the wort case she might get an entry in the Schengen Information System (SIS).