Have you tried the calculator on the website?
If you have been charged for something not chargeable you should appeal.
They charged me for North Atlantic navigation.
In Canada, only movement based charges apply for aircraft over 3 metric tons.
For aircraft weighing less, a small annual or quarterly fee applies.
See http://www.navcanada.ca/EN/media/Publications/Customer-Guide-Charges-EN.pdf
NavCanada hits you with a charge for providing IFR nav services even if below 2t.I had to pay when transiting via Goose Bay enroute Greenland.
It was pretty expensive in the Mirage – Total of about C$180.
America doesn’t have any currently, but they may come.
I hear that Canada has them – a fixed annual charge of something like $100. Is that just for IFR, or VFR as well, and what are the weight thresholds, if any?
Eurocontrol covers a larger area than just Europe. I recall that they even collect the IFR route charges on behalf of Egypt!
