What screen are they showing up on? And look at the top of the screen above the menu. Does it say "Filtering Off"? If so, click it to toggle your filtering back on.
If that doesn't work, go to the Filters screen (Tools, My Filters) and make sure it doesn't say "Replies To Filtered People Not Filtered". If it does, click it and it'll toggle to "Replies To Filtered People Also Filtered". If you toggle this, it'll also turn your filtering back on if it was off.
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