Do you have the option "Wait for card animations" set to "Yes" or "No"?
If I have it set to "Yes", when I do what you described, I can clearly see the Scrying Pool go from the supply pile to my discard pile (tested on Windows with Firefox and Chrome). If set to "No", there is some movement on the screen, but I guess it would be easy to overlook it and not realize what it meant.
Of course, if you are thinking about getting the Wharf, then I assume it will be possible to overlook the animation with either setting.
What would be possible options to make sure a player reaizes something happened in this case?
One idea would be to add some kind of glow/border effect around cards gained for a short amount of time (<1s).
Another would be to show gained cards at the same position that boons/hexes are now shown when they are revealed.