The bug

When you give yourself a potion containing the Potion tag, but not use the prefix minecraft: the game will not add it by itself.

This is different to for example entity items which get this prefix.
However it is not comparable to tags like BlockEntityTag as there the nbt data inside it is only accessed when the block is placed.

How to reproduce

1. Use the following command:

   /summon Item ~2 ~ ~ {Item:{id:"stone",Count:1}}
   

2. Using the /entitydata command you will see that the value of the id tag is now "minecraft:stone"
   This is (probably) intended as the item was accessed for rendering

1. Use the following command:

   /give @p potion 1 0 {Potion:"swiftness"}
   

2. Using the /entitydata command you will see that the value of the Potion tag is still "swiftness"
   This is (maybe) not intended as the Potion tag was accessed for rendering and for displaying the item name

1. Use the following command:

   /summon Item ~2 ~ ~ {Item:{id:"minecraft:chest",Count:1b,tag:{BlockEntityTag:{Items:[{id:stone}]}}}}
   

2. Using the /entitydata command you will see that the value of the id tag (inside the Items tag) is still "stone"
   This is intended as the item (in the Items tag) was not directly accessed as an item