It doesn't happen with recipes from Botania itself, but the crash reports always point to the Petal Apothecary. It seemed to change which mod's items are affected when I updated NEI and related mods, and Botania. Currently affects any and all recipes involving items in Zelda Sword Skills, including custom MineTweaker ones. Before I updated those mods, it affected recipes involving items from Harvestcraft and Mystcraft.

Crash Report: http://hastebin.com/korawefico.vhdl

Fffff, this is still happening >_>

So with the latest update this issue has stopped...except when clicking the Petal Apothecary icon to check Apothecary recipes in NEI (while already looking at a recipe for something in the Apothecary, I was trying to see all Apothecary recipes). Which is when I would have expected this to happen in the first place. But at least it seems to be leaving other mods alone finally.

Ignore this, a script removed an apothecary recipe, most likely what caused this.

Bug is still there. 4 years later, I am experiencing the same.

NEI support is dead in 1.8+