It's strange. Not one but it happened in 3 Hidden Grottos and my Dowsing Machine says that there's an item on the center of the Grotto.My only guess is that you're looking in the wrong place. It has to be there if your dowsing machine detects it.
I'll try to empty everyone of them and see what happens.
EDIT: Now it don't detect nothing more. Maybe it will return to normal. Thank you Slash.