If you have multiple stacks of different types of ammo which can both be loaded into your active weapon (example for shotgun 1 stack buckshot, 1 stack slugs) then holding R to reload causes ammo counts from both stacks to be reduced. It also affects the internal magazine weapons like Winchester 70 and maybe also the SKS if you have 1 stack of regular rounds, plus 1 stack of tracer rounds.
It seems to only occur when I first login, re-logging will fix the issue and the ammo stack counts will be correct. I've reproduced it with both types of shotguns and also the Winchester 70.