The bane of Space Age--production lines with varying quality.

My intent was that the normal quality items would get picked up by an inserter and fed to the factory. I put a loader at the end of the belt to dump the higher quality stuff into a container. I came back, jammed--investigation revealed normal quality items inside. Told the bots to remove/replace and the same thing happened soon again. Replacing the loader with a fast inserter with the same filter rules produced the desired result.

It appears that what is happening is that items are being allowed into the loader before the filters are applied. If so, that means that filters are unusable when the belt flows into the loader.

This behavior is by design of the game engine. So much so that we had to request and make a case for filters to even be permitted for inbound item after 2.0 was released. A loader is part belt segment. There are no filters that apply to what may enter or exit a belt segment. To remove items from the loader you'll need an inserter to the side of the loader.