This is almost certainly the result of the rule not properly un-registering hub variables it is no longer using (apps must, or at least are "supposed" to, register this use so they show up on the Hub Variables settings page; unlike devices, there is no direct reference that the database keeps between the app and a variable, so the onus is entirely on the app for this). If a rule shows more than you're using, it is likely the result of having once been used and being removed from the "in use by" list of that variable when removed. This would not be database corruption, so a restore would not help, and it also should not cause any actual problems -- though it is something that could likely be addressed on the app side.
This is unlikely to be related to your Export/Import/Clone problem, which as I noted in your other thread is also not indicative of a database problem but rather some unfortunate internal app data that can be worked around.
