Yeah, makes sense, the markers are per line, and lines exist in the document, not the view.
So per line data has to exist in the document, and per line data is where the marker number is stored, which shows as a white circle for any marker not properly set up in the view, for example in the split window view.
I don't think there is much we can do about any artefacts of interfering plugins, there have been cases of plugins using overlapping hard coded marker numbers etc.