“An unknown error occured.”
It can occur with the Better WP security plugin.

This plugin is known to cause problems with displaying available updates and also while applying available updates.

To fix this:

  1. Go to Security -> System Tweaks

  2. Under the Dashboard Tweaks section, uncheck all 3 options “Hide Theme Update Notifications”, “Hide Plugin Update Notifications”, “Hide Core Update Notifications” and click Save Changes.

The W3 Total Cache plugin is also known to create issues.
If you don’t see your updates properly, try deactivating and activating the W3 cache plugin.

You might still get the error without using the above plugins. This occurs when the plugins / themes are already updated, but InfiniteWP panel shows that they still need to be updated. It can be due to WordPress cache and this can be solved by going to the update page of that particular WP site or it should resolve itself in another 4 hrs max when WP refreshes its update section. As of version 1.1.2, you can clear the cache and Reload data to fix this issue.