Shopify theme inserting tags to <head> not showing in page source

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Hello there,

We have a live Shopify app. Once we get a subscription, we are inserting some meta tags to the <head> section of the main theme ( ...themes.json?role=main) using assets.json?asset[key]=layout/theme.liquid api call.

For one store after we inserted the meta tags to the main theme, the meta tags are visible when I display theme['asset']['value'], but not in their webpage (when we do view source of Home page). Also I can see some codes like

{% include 'seo_xxxxxxxxxxgroup' %}

inside the <head> tag.

Is anything overriding our meta tags or is there any way to know the Home page is using correct theme only?