Good day Otaku,
I'd recommend you have a look and see if there perhaps isn't any database
table upgrades that need to run as well as if the mods need an update. TO check and see if anything Moodle related needs an update, you can simply go to your website instance via a browser, log in as admin and then adjust the URL
As for the plugins/mods you can navigate to Site Administration > Plugins > Plugins Overview and then click on the "Check for updates" button. This should indicate if there are any plugin/mod updates available. Once you start upgrading those another button will be displayed on the bottom of the upgrade page that will update the effected database tables, if there are any.
Hope this helps with troubleshooting.