My '15 X Ltd does something very similar. It occurs most often after I've ridden long enough for everything to get up to temp and then stop for a few minutes. It will cut out or stumble a few times, will usually run okay when I go WOT, and then it is okay.
I believe this is from fuel overheating in the lines between the pump and the injectors during my breaks. With no fuel being consumed, it absorbs heat and boils - what we called vapor lock back when cars used carburetors. Going WOT helps clear the issue quicker since the injectors are open for longer duration and fresh, cool fuel is being pumped into the fuel lines.
If you are up for a little experimentation, you might try to re-create the misfire while you have access to a garden hose. Get it to miss, then cool down the fuel lines with water from the hose. If the miss clears up, that would suggest that my vapor lock diagnosis is correct. I've purchased some heat rejection sleeving for the fuel lines, but have not installed it.
This doesn't seem to occur on older 1000s, so I'm thinking that when AC added a catalytic converter section to the mufflers in '15, the amount of heat coming off of the muffler increased significantly.