The ships absolutely crash together; it may be pure luck that the angle means their ship did not get too damaged to sail. The ghosts are not quite as lucky, especially once part of their crew board the ship to mop up.

Considering that murdering individual ghosts isn't really on their agenda and somebody should probably mind the ship lest they try to escape on it, Levi stays behind for now, though he does keep an eye on everyone just in case they need help. So he does absolutely see Eren pull out what -- looks like a gun, just fancier and sleeker somehow -- and blasts at a ghost.

What the shit.

He considers asking that, or maybe when did you get that, or since when do you use guns, but there's not really much point to it. It's not like he has authority to take it away, nor does he think that's necessary at the moment. Eren must have picked it up at one of those fancy magic stores or something, especially since it seems to be working on ghosts, and that's just as well.

So instead he just says something like "...Nice shot," and then yells at everyone to finish cleaning up and get back on the ship so they can get clear before the ghost ship sinks.

One down, however many they still plan to take on to go!