When both guns are stowed, sights are always equipped to the "wrong" gun.

This has been an issue for a few seasons now, at least on console.  When both guns are stowed, your most recently used gun is the gun that's visible in the bottom right of the screen.  That's the gun that you'll draw if you click Y (Xbox).  In those cases, any sight you pick up will ALWAYS go to your other gun -- the one that's not visible/not drawn when you click Y.

Suppose you have an R9 in slot 1 and a G7 in slot 2.  You're carrying the R9 then you stow both guns to run faster.  The R9 is visible in the bottom right, and when you click Y, you'll draw your R9.  However, if at that time you find a Holo Sight and click "equip" on it, the Holo Sight will be equipped to the G7.  If you had a 2x on your G7, the Holo will go to the G7 and the 2x will switch to the R9.  If you had a 3x on your G7, you will actually drop your 3x to equip the Holo.  You'll realize this about 2 minutes later when you go to take a fight with your G7 and realize your 3x is gone.

In my experience it doesn't matter whether your slot-1 or slot-2 gun is in the "draw" spot.  It seems like it just always goes to the "wrong"/other gun.