Codex and Dialogue Perks not Working

I got the extra codex and dialogue perks very late in the game and have found they are not triggering the extra dialogue options.  I have seen videos of the exact same cutscenes I get and it shows the extra dialogue option with the special icon but I don't get any of these.  I have noticed this quite a lot.  Mostly on the judgement cutscenes.  I'm going to get them much earlier in my next playthrough and see if this makes a difference but does anyone have any information on this bug?