Items in Inventory GUIs need to be dragged instead of just clicked, this way it becomes hard to do most things. For example: when I try to craft an iron block,I need to click and hold iron ingots in my inventory, then one by one right-click all 9 squares in a crafting table. When I'm playing PvP games this issue often gets me killed.
I also seem to have this issue on ALL versions. I have tried reinstalling the game, I have tried both modded and unmodded (although OptiFine is the only mod I ever use), I have tried restarting the game, I have even tried restarting my entire PC, and still I am always having the bug.
Also, when I say Inventory GUIs I mean ALL inventory GUIs (chest GUI, creative inventory, survival inventory etc.)
Chck in the Controls section if you have Touchscreen mode on. Happened to me once and disabling it fixed it.