The [?] Boxes are boxes dropped by doing certain tasks. Large amounts can be obtained from downed bosses, while generally single boxes can be obtained from killing infantry (ground soldiers), S and M sized Akrid. The boxes sometimes contain weapons, emotes, Noms de Guerre and abilities, although almost all the time you will get points that are used to purchase upgrades for weapons, armor, abilities, emotes and customizations for one's character.
These [?] Boxes will contain 'credits' which serve as currency for the Lost Planet 2 slot machine. They can also contain other items such as Nom de Guerres, emotes, abilities, and weapons (rare). This machine gives randomized items out for the cost of 2,000 credits per spin; this will eventually escalate to 10,000 credits per spin. This slot machine's items include character parts and weapons only.
Boxes are obtained from defeating enemies such as Vital Suits, Akrids, enemy soldiers, and bosses. It seems boxes appear more frequently when a headshot, melée kill, or critical is performed. As a rule, stronger Akrid, bosses, and Vital Suits are more likely to drop much more boxes than regular enemies and weaker Akrid; they also tend to drop multiple boxes at once.
Three excellent sources for credit collectors are the Gordiant, supplying about 50 boxes in total, and the Overland Battleship on chapter 5-3, supplying roughly 100 boxes or 10,000 to 30,000 credits or the episode 6 chapter 4 with 122 or more boxes and 60000 credits when completely destroy the way : front, right, left,front,front, front.