When I put up, put the bike in neutral, flip the side stand and then climb off leaving the engine running. about 50% of the time the engine cuts out! Not a real issue as I am about to turn the engine off anyway just really know why the bike does it
I would take a look at the neutral switch, the sidestand (possibly clutch) switches for any damage or wiring problems. I can't remember if Honda tie the clutch switch into the cut out circuit for being in gear but I suspect that's the area you should be looking at for your fault!