I've never heard of that. I've stayed at a few places where there is a small supply included and then a note that additional pods are charged. While that seems chintzy, I suppose a property is free to do what it wants.
How much were the pods/bags priced at in the room? If they were priced at EUR 3 and you used them, I agree that it's chintzy, but your choice.
If the price or the fact that there is a charge is not apparent, I would be interested in how you dealt with this at checkout.