Why are plugins with the same name and version grouped differently in WP Toolkit on a Plesk server?

Question

Why are plugins with the same name and version grouped differently in WP Toolkit?

Answer

This behavior occurs because the same plugin is installed through WordPress and by uploading the plugin archive manually. Manually uploaded plugins have a downward arrow icon next to the name. Plugins installed in these two different ways do not group together.

As a workaround, detach the sites with the manually uploaded plugin and then reattach them in WPT. Then WPT will consider that the plugins have been installed through WordPress.