I just did some additional discussion and I need to verify if you are using Mattermost Team Edition or the Paid Mattermost Enterprise edition. if you are not using Enterprise Edition (with a valid license), you will be unable to enable High Availability / Clustering mode. without HA enabled, you will definitely experience that kind of notification weirdness with multiple MM instances talking to the same database while you’re waiting for the other server to catch up. if you’re on team edition, my suggestion would be to drop the second instance and remove mention of it from your NGINX configuration. This will almost certainly resolve your issue.
Sousapro.