It's possible that you actually sold the 2 artifacts to the Museum, as apposed to
donating them. I made this mistake on my first Tribunal playthrough.
Normally (when not on this particular quest), you have 2 options at the museum: Sell an item, or just keep it. When this quest is active, a third option is enable: Donate the item. You won't get any money for donating, so make sure to donate artifacts that you don't like.
Do you remember if you were paid for the items? If you were, this is where your mistake is.