I don't know if this explains all the duplicates, but at least that particular example is due to Bill Waterson's sabbaticals: The last result from May 21, 1994

I don't know if this explains all the duplicates, but at least that particular example is due to Bill Waterson's sabbaticals: The last result from May 21, 1994 lies within the period of his second sabbatical – April 3 through December 31, 1994. For those two periods, Gocomics is simply filling the gap by repeating earlier strips (and I think the same thing happened during the strip's original newspaper run, too). So if you didn’t knew about those sabbaticals (or forgot about them), it's easy to accidentally include those duplicate strips if you were to just blindly process everything between November 18, 1985 and December 31, 1995.