Yes, this happened to a couple of my Caxton card withdrawals back in February - I think it was a blip then because the charges were refunded, and at that time, at no point did the ATM 'tell' me it there was to be a charge.
This is different, but it does seem ATM withdrawal charges are in force at some banks here. We have been informed on the display of a charge at Piraeus (EUR3) and Eurobank (EUR2.50), for the last week or so now. So far, in Chania, Alpha and Bank of Chania have not charged (maybe a matter of time?).