I mean, really, where in the series is it said that there isn't a phaser emitter mounted on the photon topedo tube? It isn't a mistake just because the technical advisors of the show or a fictional Technical Manual say so. So again, I wouldn't want them to change that.
Where in the series is it said there isn't an energy beam emitter mounted on the captain's yacht?
The shot in Darmok is one of the more notorious bloopers in TNG. CBS-D fixed the energy beam shot in the pilot. I'm sure they'll redo the one in Darmok too.