When you go on missions in Avenger's Initiative, pressing up on the D-pad reveals a bunch of questions marks located around the map other than just the main objective. If you just go towards the main objective you will miss a lot of these so take these solo or a team that will go exploring with you. Most of them have chests but a few have aim prisoners.
Depots are buildings that have an unbreakable locked door with 4 yellow lights at the top or sides of it. These doors are opened with a timed button pressing puzzle. The timer is 30 seconds and starts when the first one lights up blue. There are 3 ways, so far, to open these.
A) Some are yellow pressure pads that you have to stand on scattered around the area. When you press up on the D-pad they should have a yellow line connecting them to the door.
B) Some are white consoles with a yellow hexagon against walls that you have to melee until they turn blue.
C) The last puzzle type are yellow gears on walls or in vents that you have to shoot with a ranged attack.
When you hit all required switches (usually 4 but a few in Eastern Seaboard are just 1), they will turn green and the door will open.