I had the exact same issue when I figured out that it occured when I would hold down the shift key and auto loot really fast. TBH I forgot what exactly I did...I think I unbound some shift keys out of the keybindings menu...
Either way if this is the same reason that it is causing it for you, you can simply go into interface option and and turn on auto loot. There is another way to fix it but I can't for the life of me remember atm what exactly I did...