I've noticed this a couple times now while fighting Zeniths in a Gropho.  What happens is during the missile cycle/cooldown a couple missiles will 'fire' again, but the explosion happens instantly on the target, and no trail or firing from my mech is seen.

At first I thought this was just some visual bug, but the second time this happened I noticed 2 of my launchers had a lower ammo count when I reloaded.  I knew these 2 particular launchers should not have a lower count because of the typical ones I keep running when I need that extra shot or 2.

I'm really not sure if it expends the ammo and does damage as well, but it doesnt seem to interrupt the normal cycling of the launchers at all.  This has only happened to me a few times, but it was always while fighting Zeniths, so I'm curious if it is somehow related to their ECM's or some other e-war thats being used on me.  Now that I think back on it, the timing that these have happened in (about 2/3 seconds after my first salvo) coincides with the enemy finishing its lock-on and firing the first modules.