Cancel that Series Recording and do it again. Only on the 3 programs that are doing the multiple-recording.
When i set up a Series Recording for only "new" shows, i saw some times where the tv guide did not list an upcoming show as "new". I set a recording for that show by hitting the red Record button. A single checkmark appeared next to the guide listing. I later saw that the show had been recorded twice. It seems like the tv guide updated to mark that show as NEW. So it recorded once for the Series Manager (which shows 2 checkmarks) and once again for my selected recording.
The point is that there can be little quirks like you mention.