I think I know why this happens, correct me if I'm wrong. When an outlander dies, the non used ammo from the gun gets into the inventory. The ammo is the most "important" type of item, because when you loot something, using the (X) button, the first thing that you will pick is the ammo. The crate is less "inportant"(dunno why) because when you loot it from a dead body, using the (X), with 1 or 2 free space in the inv, first you will pick the other items(meds, ammo etc.) instead of the crate.
If an outlander takes the crate and his inventory is full, and you kill him, the ammo which was loaded into the gun will get into the inv, BUT if the inv is full, the less "important" item will dissapear, which is the crate.