Thanks for reaching out in our Community forums. I’m happy to help.
I understanding you are having a few issues when submitting your sitemap for your store. This Google help doc covers this topic. Essentially, the "Indexed, not in sitemap" message indicates that the URL was discovered by Google and indexed. Did you follow this guide to submit your sitemap.xml file? This should be the only sitemap that's submitted. If you haven't submitted this particular sitemap file, then this could be why you are receiving this message. Please Keep in mind that when you submit your sitemap, it does take anywhere between a few days to a few weeks for Google to be recrawl it, so you will not see the status change immediately.
Let me know if this helps!
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