One of the crates is labeled "Shotgun Ammo" and the one next to it is labeled "Shotguns". The crate labeled "Shotguns" opens when Chloe rolls next to it. 

Xeno turns as he hears the ship leave seeing the crates and the skull attack Chloe, he runs towards the crates and shoots the Skull. Upon reaching the crates he turns and shoots the last of the Skulls. "You alright recruit?" he ask Chloe.