Hi there,
At first I’m not sure what would be adding a bunch of custom notes like that. Those are the ones that are blue as normally a payment method will leave a private note like you see here from Stripe compared to my customer note in blue.
Link to image: https://cld.wthms.co/8GjiH6
This is likely caused by a conflict with your theme or with another plugin.
The best way to determine if the issue is being caused by a theme and/or plugin is to temporarily switch your theme to Storefront (https://woocommerce.com/products/storefront/?aff=10486&cid=1131038) and disable all plugins except for WooCommerce. Finally, test to see if the issue is resolved by placing test orders and watching for any repeating order notes like you were seeing earlier.
If you’re not seeing the same problem after completing the conflict test, then you know the problem was with the plugins and/or theme you deactivated. To figure out which plugin is causing the problem, continue to the next step. Reactivate your other plugins one by one, testing after each, until you find the one causing conflict.
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Tools to help you troubleshoot:
Meks Quick Plugin Disabler is a plugin you can install which will remember what plugins you currently have active so it’s easy to switch them back on. Link: https://www.ads-software.com/plugins/meks-quick-plugin-disabler/
You can clone your site to a staging environment and perform tests without modifying your live site or impacting customers. Many hosts provide staging facilities, so it’s worth checking in with them. It’s also possible to do it using the free WP Staging plugin. Link: https://www.ads-software.com/plugins/wp-staging/