Are you sure it's not just that your card has both EC and Visa Electron/Mastercard Meastro or similar, and that it's the EC part they accept?
It's been a few years since I've been to Germany, but for comparison, in Norway - while it's nearly unheard of now - you also used to be able to find places that'd take "BankAxept" bank cards, which would be pretty much every domestic debit card, and is similar to EC Karten, but not Visa Electron/Mastercard Maestro debit cards.
If you had a domestic debit card, you'd almost certainly have a Visa/Maestro logo on it as well and so it'd be easy for people to assume that was what they were paying with.