I have had occasion on my '05 Chopper and my HD's (RoadKing and Softail Deluxe) to have the same thing occur. I would be stopped and try downshifting but nothing would happen, other than the shift lever moving.
I found that easing the clutch out (to the friction zone where it just barely engaged) and squeezing it back in corrected the issue. I think it maybe has something to do with the transmission gears being synchronized or something. It only happens occassionally and I don't think (in my case) it is a concern.