I've had the same issue, occasionally since purchase (brand new 2014 6MT). At first I thought it was me getting used to a different kind of car. My old 350Z (which I had for 10 years!) really liked to be thrown through the gears.
Now I think it may be related to a similar problem we had in the 350Z world. Forgive my ignorance as to the part's exact name, but there is a little shifter plate inside the shift boot, that acts as a frame -- guiding the maximum range your shifter can go in any direction. Sometimes these would be put in too far to the left from the factory, or bump left over time, causing the shifter to "wander" too far left and cause binding or missing the gate. So I may check this out when the issue becomes more common. I'm in your boat as to allowing Honda service to do casual repairs. It really seems to cause more headaches than it solves!