I think the official thing to say is that items are bugged.
I cannot retrieve bolts after I fire them. Infact, I find that there are many instance where I cannot pick something up though I right click and choose Take alot. I have found 2 ways to deal with this. 1. If I walk away until the item is out of sight, I can walk back upto it and take it. 2. If I do anything with the item other than take it.
For instance, with bolts, if I empty my crossbow and choose load ammo on the bolt on the ground, it goes right in, then I can eject it and put it into my inventory. It is like there is something broken with taking certain items.