I tweeted about that miss as it happened... if I'm remembering correctly (and who knows if I am) it was a long third down, and as the video showed deep in our own zone. So MAYBE Goff was looking for a more sure thing, in the 10 yard hitch for the first down. Yeah, I know he has good deep ball accuracy, and you gotta take it if its there, but maybe sub-consciously he was thinking about moving the chains, and not going for the TD. Like, "this is the play call, and Watkins may be open for a deep throw... but it might be easier to throw it ten yards and keep possession." If he's still a little unsure of himself he may have been mentally leaning toward the safer play.
Just a theory.