KillingMoon, the mushroom shouldn't have disappeared if you didn't have a high enough level to create a potion. The flask should have gone back into your inventory.
I just tried it again; just hovering the flask doesn't make anything disappear, but if I hover
and let go, then both the mushroom and the flask disappear, and at that moment my character sighs 'Ugh, I'm obviously not skilled enough to do this.' Must be the way it's disigned.
Regretfully I didn't have another skill point to invest to see how to do it the right way. Anyway, thanks to your help, the question is now certainly answered!