We had an issue with Calendar (Event) lists specifically, whereby recurring items would count as more than 1 actual item. But this only affected items past a certain date, it was really strange. We also couldn't open instances of the recurring events past that date, since that triggered a list-scan/threshold error somehow. We opened a ticket and got nowhere. They gave us the "this is by design" crap when they know there's a problem they can't fix.
We ended up having to migrate "older" items to a separate list. This fixed the issue, but now our users have to search multiple places if they need those things. Feels bad.
Not sure if this applies in your scenario, but just know that the threshold has some quirks (maybe you found a new one!). As long as the filter narrows the results down to below 5000 items, it should be good. This is 5000 items total returned in the view by the way, not just "per page".