If it is right below the surface, you can smack at it with the butt of your rifle (or maybe even fists) and spamming the pickup key.
Worked in mutliple occasions for me.

Molly, my most trustiest of mules!

real usefull info found several maps whit items stuck in the walls or under the floorboards. or in the roof after blowing up a barrel in a store whit shelfs

Now this is useful info thanks