My gut feeling was that it happens after a mass disenchant followed by a logout. The cards that you had copies of getting disenchanted after a pack opening or more, assumes the original copies being DE’d and after you open the list, it corrects itself.
This thing began with the patch before sn1p-sn4p. The offline collection mode is the perpetrator if I had to take a wild guess.
And yes, if you go to play mode, do not click on your deck to auto-fill it. It actually removes and adds cards on it’s own volition.