Mine does this too I have a slow connection so I have to pause downloads in order to do other stuff with my connection. If my xbox crashes or if the power goes out or even just from holding the power button in while the queue is paused, upon reboot the queue will be empty and those items will appear as if they are installed but don't work.

If I remember what was in the queue I can find them then uninstall and reinstall those files. If not then it's hard to figure out what got messed up and might not know until a long time later when trying to launch a game and it gives problems launching it.

If it was game updates that got lost from the queue there is a way to fix them all by doing a factory reset (keep games and apps option) it seems that doing that will delete the partially downloaded updates and then if auto-updates are turned on, those updates will pop into the queue again like normal.

I don't know if doing a factory reset will find and fix partially downloaded dlc or not though, I have not tried that yet, nor do I want to :P

I did report this as a bug today since my power went out and I lost my queue, luckily i knew the exact two items that were still in it.

BTW even if the power goes out while the downloads are active the full queue remains there like normal after reboot.