if you mean that using the ammo crates causes the ammo to spill out over the ground, then its a well know bis problem, known as the "Ammo Bug".
It's basically causes by overloading the ammo cargo of a vehicle/ammo box etc.
3 possible methods to stop it
1) Dont overload ammo crates, especially with secondary weapons
2) Use a mod, that has it's ammo crates cargo capacity increased, or use an addon ammo crate that has its cargo space increased
3) implement the "CTI clean up ground" addaction method
Option 1 is the best idea, just place more ammo crates on the ground with less in them and remove all the cargo space in any vehicle
(see comref for how to do)