I've been replaying Gothic 3 and several walkthroughs I've looked at all say that Stoneroot plants don't display in inventory. Actually, they do, but not in the tab you'd expect to see them. They are NOT shown in the tab that displays the healing and mana plants and potions. Rather, they can be found in the next tab, Miscellaneous, where saws, hammers, weapons bundles, wheat sacks, fish barrels, etc are displayed. If you look closely you will find a label and picture for Stoneroot and how many you actually have collected.

Tom