You should complain to the seller, and if it doesn't work, to the shop director. The law states that the price from the shelf is important, not what is saved in the memory of the till.
In bigger shops it's sometimes met that when the customer waits at the service point for explanation, they quickly change the label on the shelf to show them that they were wrong :)
And they will probably try to make difficulties when you want to complain, because it's difficult for them to register on the till something with changed price or with fractional amount. Which is very easy in case of a foreigner, they can just say they don't understand you. But it's always worth to try. Maybe you meet helpful staff.
Related: System of barcode in Poland?
wot is the system of barcode in poland.. i have products and i am supplier.. where and how can i manage barcode for my product..
In the whole EU it's all EAN13.