Ok, you probably know the plot thread I'm talking about. I'm in Chapter 3 and just saw a cutscene calling Stennis the poisoner of Saskia but evidence found in the quest did not prove his guilt. It was made clear that the priest was 100% guilty but not Stennis.

Is this a hole in the writing? Did I miss something?

I think it's not supposed to be that clear. From my memory of the evidence I saw, it seems like he did it but there was someone else involved. (LATE GAME MINOR SPOILER) You find some evidence at Phillipa's place later in the game that suggests she was the one pulling the strings, although I think she denies involvement, for what her word is worth (jack shit).

Also not sure how the quest played out for you, but I think you can miss some evidence and stuff. Not that it ever says HE DID IT but if you get all the evidence seems very likely that he did.

But I think the whole idea is you kind of have to go out on a limb on this one.