Anything should be susceptible to alt-click, even if it isn't stackable. If a stack of some non-stackable item is broken with alt-click, the game appropriately marks that item as being non-stackable. Currently the game only seems to do this check when loading a game, so stacks of non-stackable items become non-stackable again on reload, but they also can't be broken, leaving the items stuck in the stack.
(Crafted items shouldn't be stackable in the first place, other than consumables.) We've had this bug filed internally for a long time.
