I have chosen to display 50 questions per page on Stack Overflow. However, as I have added "Ignored Tags", the number of questions per page has shrunk (for example, a few moments ago I could page through 5,790 pages, but the first page only has 14 questions when it should have 50). Ideally I would think that the result set would be filtered first, and then pagination applied. As it is, pagination appears to be applied first, and then the result set filtered, resulting in fewer questions per page than a user (me) would expect.
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The problem is that the filtering is client-side, and all it is doing is setting display:none to the question. If it was all done on the server-side (or you were fetching client side) then perhaps something could be done. But as it is now, you are ignoring things that are already there. It is not stopping them from actually getting pulled back from the database.
Just bringing this back to the surface to highlight the issue with the current League of Legends contest over at gaming.se. Hiding just league-of-legends (zoomed for emphasis, also there is a bug in the sidebar when zooming):
9 out of 50 questions being displayed.