If you compare 2013 and 2014 transmissions on one of the OEM parts websites, you can see that Honda changed the part numbers for three parts (mainshaft gear 2/3, 4, and 5) in 2014. Somewhere on the web I saw photos comparing the old and new parts. Honda clearly knew they had a problem, though from what I've read it's pretty rare, like the rear brake issue.

I've only heard of a few reports where the ghost shifting actually caused damage. Those cases were bent shift forks.