Canon inkjet printers do not contain any mechanism to measure the amount of ink left in a cartridge - any values that the printer or status monitor give you are estimates based the number of pages printed since the cartridge was last changed.
The Canon status monitor is unusually difficult to work with, and will often report cartridges as empty or low on ink when they have just been replaced. This can sometimes prevent printing altogether.
You may see a graphic representation on your screen that looks something like this:
Older models have a numeric error report, you may see the error codes U162, U163, E005, or 1401 - there are others, this advice refers to any error that your manual informs you is related to ink levels.
The easiest fix is to turn off the status monitor. First, locate the button that will do this - it's on the front panel of the printer and may be marked "STOP", "RESUME", "CLEAR", "RESET" or any combination of these.
The symbol is always the same though, it's a red circle enclosing an inverted triangle:
All you need to do is to hold this button down for 5-10 seconds. The printer will usually beep to acknowledge, but this varies from model to model.
Depending on your printer model, you may need to turn it off and on again for this to be registered, and you may also need to repeat the process for each cartridge.
When you have done this, you will no longer get reports of empty cartridges when they still contain ink.