The rifles are switching shoulder when you switch from one rifle to the other since update 1.09.
In 1.08 the rifle stayed on the side you assigned it to when you switched weapons. Witch is logical. If you take the right shoulder rifle out and want to change to the left after. It makes sense that he would put the rifle back on his right hand shoulder before taking out the left shoulder rifle.
Now in 1.09 if I take out my right hand shoulder rifle and want to switch to the left he puts the right shoulder gun in the same spot as he takes out the left shoulder gun from. So at one point he technically holds 2 guns in his hands before putting the first gun in the wrong spot(left shoulder in this case).
This might not seem like a big deal but since the shoulders have different draw times, it is a big deal to be honest.
For instance, I have my close encounter rifle on my left shoulder for a quick draw and my sniper on my right hand side for the slow draw. But now in a gun fight, both of my guns are just switching from the same slow shoulder so I'm always drawing the gun from the slow side after the initial draw.
Please make it work like in 1.08 again, have all the guns go back to the same shoulder/slot it was drawn out from as the first option. It both just make sense and is how it would be done if you're going for realism.
Same with handguns, have them first go into a holster if one is on your character(same one as drawn from if multiple holsters are present). Then into your inventory last if no holster is there at all.