I'm not sure if this helps, but we have merchants face this sometimes when using Intuitive Shipping. Our product specialist created a Help Center article about it, which may give some insight into the problem and how to correct it (there's a link to contact Google near the end). It's the same if you're using a third-party app or just Shopify's shipping, so I hope it helps
You can manually add shipping prices in Google Merchant Center if the automated method does not work.
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