Fixed on your site and in the next release. If "Any Type" was already saved redundantly with other types checked, then subsequent attempts to remove "Any Type" would fail until "Any Type" was first saved as the only selection.
I should note that removing "Any Type" from the System area is contrary to the purpose of the System area, which is supposed to be a fallback location for all content. Changing the type-rules limits what admins, install processes, and imports can do there. Ideally, if the desired effect is to prevent regular users from creating new content there, permissions should be used to restrict new content in the area. Since your wiki is already established, this may not effect you; however, future features which will rely on the System area may ignore your custom type restrictions.