Hmm...
Sounds to me like you've filled your ammo crate up so much that you can't put anything more in it!
Since Resistance (I think??) ammo crates have a capacity of:
- 1000 weapons
- 2000 magazines
So if the number of weapons in your ammo crate exceeds 1000, any you try to put in will end up on the ground (that includes any you try to 'swap').
The way to stop this from happening is to reduce the number of guns you've got stuffed in there, mate ;)
You may need two crates instead of one