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Does the platform you are using let you select a default category for the product? Several platforms will let you select multiple categories and make you chose one as a default category. If so, you can just work off the uri of the page and insert the default category as the canonical category in the rel=canonical.

Hi JDM, Thanks for reaching out! My name is Erin, and I'm on the Moz Help Team. SilverDoor had some good advice. Can you email us at help@moz.com and let us know which campaign(s) you're experiencing GA issues with? We can help you troubleshoot this from there. I hope this helps, and we look forward to seeing your email! Cheers, Erin