Google Page Indexing - most pages not indexed

[JoesToes]

I've had my shopify store for years. I'm always looking to improve.  I have recently noticed that Google says the vast majority of my pages are not indexed for this reason "alternative page with proper canonical tag" . I wonder why this is  - and if it's a problem. And if it is a problem how to address it?  Not sure if this is relevant but most of my products come close to the 100 variant limit. 

[JoshHighland]

I'm guessing these are collection pages that have tags. The canonical tag is going to point tp the collection, not the filtered tag. 

You can do this by updating the canonical tag code in your theme, but you are going to run into an SEO issue of the title and meta description being the same as the base collection.

The best way, and only app I know to support this, is SEO Manager. It's my app but I built this feature to help folks like you. It free to install. There is a link in my signature.

[JoesToes]

Is it a universal issue? If so your app will surely be popular. I can't decide if it is worth worrying about and adding another app.