I am a Canadian with dual citizenship that left Canada without using my Canadian passport [duplicate]

When booking the ticket, I entered my Japanese passport number and from what I’ve read on this forum the airline then notifies immigration that I have left the country. But as I never entered Canada using the Japanese passport in the first place does this cause any problems?

The passport you use when booking the ticket is not particularly important. The passport that matters is the one you use when you check in for the departing flight. In this case that will be the same passport, of course (the Japanese one).

It should not cause any problems. Canada will probably be unable to find a matching entry record for your exit record, but that is a failure of their recordkeeping systems to account for dual citizens. You haven't done anything wrong.

How should I book a flight back to Canada?

With your Canadian passport, of course. You can't use your Japanese passport to fly to Canada, because you would need either a visa or eTA authorization, and you cannot get either of those things because you are a Canadian citizen.

There is no requirement that you use the same passport to enter Canada as you last used to leave. It is very unlikely that you will be asked about your seemingly lopsided travel history (though I suppose the likelihood may increase as systems for recording and reconciling entry and exit records become more comprehensive). If someone does ask, you can just tell them that you used your Japanese passport to check in for your flight because you were flying to Japan.