Thank you for contacting us. I am happy to help you.
In our systems I can see 3 registration in the same domain :
hidden link hidden link hidden link
This is not correct for me because you should have 1 registration per domain, except each domain of the above, are having a separate installation of WordPress which debug info you shared is not indicating something like this.
You should have only one key for hidden link. If you are not sure , please go to your installation, and unregister the site. then go to wpml org account delete the rest keys and create a new one. Register again the site with that key.
At the end go to your installation WP > Updates and clik a few times "Check for updates" link.
Then check if the message is gone.
I hope this helps. Please let us know how it goes or if you need any further assistance. I'll gladly help you. 🙂