I have been playing through The East Wind campaign and I've had some of the items lost or altered when returning to the camp after a mission in the second act (Adapt). I don't know if it also applies to the first act.

During the first scouting mission in the second map (the one from Bomos, happening at night), you are able to optain several black MX rifles. After returning to the camp with these rifles, however, they all turned from black variants to the standard sand variants after being transfered from my scouting vehicle to the weapon crate. Also, on a side note, since we're given black MX rifles, I think the ammo magazines included with these rifles should also be black but that's a suggestion more than a bug.

Another bug is when you return to the camp while carrying a backpack and having another backpack inside of that backpack, the backpack inside of your backpack disappears from your inventory. Example: I'm equipped with a Caryall Backpack and I have an Assault Pack inside of my Carryall Backpack. When I return to the camp from a mission (be it a scouting mission or a regular mission), the assault backpack disappears from my inventory altogether (it's not deposited to any of the crates).