I just thought that if it had been openly active that recently, the characters in DS9 would have at least been aware of them, but it DS9 nobody had ever heard of the organization at all.
It wasn't enough to effect my overall enjoyment of the season, which I loved, it was just the one thing that bugged me with the story.
Well, people in "Encounter at Farpoint" seemed surprised by holodecks, even though they had one in TAS, and even though VGR later established that Janeway had played holoprograms as a child. Trek continuity has never been anywhere close to airtight.
Granted, yes, an open Section 31 does create a degree of inconsistency with DS9. But it is a whole lot less stupid than the conceit that S31 somehow managed to be both far-reaching and totally secret for over 200 years, so I'll take the tradeoff.