Is it happening when you move the shifter or when you disengage the clutch? I have driven five 2016/17s and the gates on the gear box are all different, some are silky smooth in and out and some you have to "pop" in and out of. Sometimes it almost sounds like a grind and 3rd seems to be the one that mimics that the most. p.s. mine is the worst of all five i have driven, on very cold mornings it's hard to go through the gears the first time.
I agree it's weird that it doesn't happen at redline/WOT. My new '07 Civic SI grinded going into 2nd gear at redline/WOT (as did almost everybody else's).
So it happened when clutch was in, and I moved the shifter from 2nd to 3rd. As I was trying to get into 3rd, I heard the grind. It acts more like the clutch isn't fully disengaged. The first time I thought it might be user error (i.e. clutch not all the way in) but the second time, I know for a fact the clutch was all the way in because I was conscious of the issue.
I have a Sport and same thing is happening to me. Started at 500 miles. At first I thought it was driver error but I've tried different shifting techniques and it still happens. I feel it in second gear as well. It really feels more like a rough shift than a grind but I do hear a fairly loud click when it goes into third. It only happens when I'm cruising.
I have a 16 LX sedan 6MT. I've noticed that until the tranny fluid gets a little heat into it I get a little grind in 2nd and 3rd. Seems to be worse the colder ambient temps. On a really cold day it'll take 5 miles or so. On a warm day it takes 1/2 a mile. And on a hot day it takes about 1 shift into each gear.
Keep in mind this thing is 10x better than my T56 will ever be. (V8 muscle car)
I haven't noticed any problem yet (4000 mi) with 3rd on my 2017 LX Sedan.
Vent warning: What happens to me that I do hate, is that going from 5th to 6th, it wants to shift back into 4th. I have to really make a deliberate effort to go into 6th.
(no grinds or anything).