Sometimes, after re-syncing, the list of available updates includes plugins or themes for which the available update displays the same version #, thus there is no actual update to perform. I sometimes have to re-sync a few times before they remove themselves from the list.
I have see this both in the dashboard and in the Daily Digest email I receive
Yes, I’ve seen this as well and most of the time with premium plugins/themes like Thrive. These updates have also display issues on the website, so I think that’s also playing a role. The site gives some mixed signals. I’m not sure if this is something MainWP can solve (hiding it at most), but that it should be fixed by the plugin/theme author by fixing the integration with the WP update process.