After a long wait at border control, which caused us to miss our ferry, we found out that the issue was to do with the EES not recording her exit from a recent holiday. This meant that, although she was back in the UK and at school, she was flagged as overstaying. Border officials weren’t very understanding about the issue, claiming we should have checked that she was marked as exiting the EU, although without passport stamps, there’s no way to do so.
Penalties for overstays can vary from country to country, from a couple of hundred Euros to the thousands, and you can also find yourself barred from entering the Schengen Area for up to five years.
I contacted the Foreign, Commonwealth & Development Office (FCDO) to ask them what to do if you are flagged as an overstayer due to a system error or oversight, as was the case with my daughter.
It advised passengers to read its EES Travel Advice page, which says that travelers can contact the supervisory authority of the European country using the EES in charge of processing data.