It is really a glitch - you have nothing to do with it.
I had another glitch - almost like yours. You know, that you can imrove HK-47 by talking to him? (spoiler?). And when you "repair" him a bit - he gains some minor improvements. And when the dialog with him is over, the game writes to you a message "Item lost. Item gained."
But noone ever saw these "Items" - they are considered "HK-47 only" and do not show in inventory.
But in my last walkthrough I actually got them. It is an item of sort - you can not equip it anywhere (HK included), and it does not have an icon - just the letters "HK-47".
So I had to carry this item in my inventory - I could not even sell it.
And HK had not got any uprades by the way. (Although the Quest Journal said that he should)
This game is full of glitches, it seems...
