I've encountered this too.
Here's how to reproduce: Put one torch in off-hand. Go to crafting table, and prepare to craft torches. Shift-click them.
I expected this would stack with the torch in off-hand. (This does happen when I craft torches without a crafting table). Instead, it creates a new stack.
Does not duplicate MC-84224! That one is about using shift-right click to place a block on a usable block, not about shift-left clicking to move a whole stack.
What was your world seed? And did you create this world in Minecraft 15w34d or an earlier snapshot?