It just started happening yesterday in a new game, and is the first time I’ve ever had it happen, so I thought it was new. I didn’t do anything different from last game, except added Extended Realistic Guns mod and Urban Development mod. The bolts are just auto placed into the quiver when you pick them up, even with auto pickup off. I’m guessing you have to have a quiver available for them to go into, but that should be pretty obvious.
Also a quick way to add things to your auto-pickup, hit ‘+’ aka (‘shift’ + ‘=’) while examining the item in your inventory, which sets it to be auto-picked up. Then hit ‘Esc’ then ‘3’ to go to pickup manager then ‘Tab’ then ‘shift+M’ to move it over to global, then ‘Esc’ then ‘Y’ to save.
You can also just hit “p” in the advanced inventory to add it as an auto-pickup rule(I believe it is ‘p’, but just hit ? in Advanced Inv if not to find the correct key or maybe set it if it’s not set by default)
For arrows and bolts I just added arrow and bolt to the global list.
You do need to turn it on, either through options like was mentioned, or you can do like I do and just hit Esc+ 3 + s + Esc while in game to turn it on or off quickly, which I do before entering my base usually so I don’t pick up a bunch random parts from my crafting station.
I don’t like the pick up small objects option, but YMMV, Also, there is an option to turn off auto-pickup when safe mode is off, I use that option, so that I can hit ‘!’ aka (‘shift’+1’’) to turn it off while in a fight so that yo don;t try to pick stuff up while in the middle of battle.