Crates are powerups present in all Command & Conquer games.
In campaigns, crates are pre-scripted on battlefields. In skirmish and multiplayer mode, crates are a kind of "scenario condition" that can be switched on/off before game starts. If switched on, crates randomly appears on battlefield and, if not being picked up, will vanish after a certain time.
To pick up a crate, simply order a ground unit (if it's on water, order a ship or submarine or amphibious vehicle or anything can move on/beneath water) to move to its position, mind many crates have field effects.