Just noticed this glitch today (might be after latest update), but when I drink potions directly from my vault, 2 potions disappear at once. Everything is fine, though, and the numbers are correct. Seems to be a visual glitch? I have to re-enter my vault to drink the correct amount of potions. Here is a link to my recorded vid:
Update: if my inventory is full, and I double click to drink the pots from my vault, it works fine. It only does the glitch when I shift click.