You can't put magazines or fast loaders into ammo boxes. You used to be able to do that.
I also was in a situation where I had a single round of .45 ACP ammo and wanted to put it into my ammo box, I couldn't. I have not tried the single round thing with other types of ammo.
I don't know if this matters but the 1 round of .45 had been chambered in an FNX and then removed while the FNX was on the ground, the single round was then picked up. It shouldn't matter but who knows.