The Crates can be found laying next to the Verdant Meadows airstrip. If the player runs towards them, crates will hit the player slightly damaging Carl. If the player runs on them constantly, they will eventually cause Carl to die.
The crates are in fact programmed as a movable debris. Same happens with trash bags, tires, and windshields (if the player constantly stomps on the hoods, while on cars, windshields will fly off and hit CJ, resulting in him losing a bit of health,) thus making the behavior of the crates game-mechanic induced.