This happens with the crafting table.
You want to click very fast in order to get the crafted things but after some fast clicks the game will stop reading clicks.
Instead if you click very slowly it will work well.
Example.
Go to the crafting table willing to produce sticks from wooden planks. put the planks in the right position then click faslty to get many sticks. It will stuck.
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I have the same problem
Confirmed in 13w01b.
This is particularly noticeable when trying to get the right enchantment level on an enchantment table. Usually I just keep placing and removing the item in the table, but now this must be done extremely slowly in order for the click to be registered. The problem also seems to get worse when vsync is enabled (maybe it's just me).
I found a workaround to craft less than a stack: hover over the crafting result and tap a number key to craft to the hotbar as much you need.
It seems as though the click handler is now triggered on mouse up (when you release the mouse button) instead of mouse down (when you press the mouse button). This creates a problem when moving the mouse rapidly as the game will either think you are clicking elsewhere or dragging. I suspect this is a by product of the way the new inventory drag features were implemented. I have been able to avoid the click problems by being mindful of where my mouse cursor is when I release the button but that results in painfully slow inventory management and crafting.
My comment in MC-6384 also applies here.
Shift-click?
Edit: I guess it was fixed in the new snapshot, so never mind.
I checked this in the prerelease. It is still not fixed.
Nathan Adams
this is probably due to the feature where, if you double-click an item you get the items stacked. It shouldn't do this on the output of a crafting table though