I'm not too sure if I had done something wrong or not, but it seems as if potions are no longer stackable as of some of the recent snapshots (not too sure which one) with the /give command. Is this a bug? Or a feature change? If it was a feature change then that would seriously mess up a lot of PvP maps, including a derpy amateur one I'm working on right now.
If I want to do
/give potion 64 16428
It will give me a full inventory of Splash Potions of harming (the correct id) but they will each occupy a slot separately (won't stack) as if I were in survival. However, before this change, if I did the same command, I would desirably get 1 full stack of 64 splash potions, occupying only one slot.
I believe that's a feature, since potions aren't really supposed to stack. However, if you know which items are going in each slot, then you could use the new /entitydata command to set a particular slot to a stack of potions to achieve the same effect.