Seems to depend on the server, if it is on heavy load it will put your missile weapon on cooldown, but no missile is fired. The cooldown is only visual though, you can click again and your missile will be fired. Seems to be fine for other weapons.
I managed to reproduce it consistently when firing a missile near a planet, around 0.5-1 second after you typed /force_save.
How to reproduce (or try...):
# go near a planet or something big
# /force_save
# shoot your missile shortly after that (don't do it too fast, maybe 1 second or a little bit less after entering /force_save)