I get this too, but for me at least it has nothing to do with clicking too fast. It happens on draws, whether from SD or Hourglass, or just a normal draw. However, every time it's happened to me, I haven't clicked on anything since drawing.
For example, one time (at band camp...) I drew my card directly after my opponent's attack (no clicking). Card shows up (pillar, creature, whatever), card goes to hand, card disappears. Only once have I had a 'ghost card' show up, though, where the card is still residing in a hand slot so that newly drawn cards are shown underneath this blank space (the other times I couldn't draw past 7, was told to discard at 7, etc, but no placeholder was kept, the newly drawn cards just kept stacking as normal)
As I said, no clicking was done, no cards played, no extra draws, no nothing, just a disappearing card.
This has happened a total of 4 times to me so far, over the past 3 weeks.