I have encountered this issue many times, but have not been able to reliably reproduce it. There seems to be a case where a skeleton spawns, but has no sense of aggression towards players. If hit, it seems to take damage, but only once and then fails to respond to anything after that. Prior to being hit, it seems to be AFK, never responds to the sun or outside stimulus. The spawning of this type of skeleton seems to be random and has not been seen in any other type of mob.
Confirmed that this still occurs in 1.9 Pre release 3. If I craft an item using either the craft table, personal craft table in inventory, Anvil, or Furnace and attempt to acquire it using a hotkey it only works when the slot related to the hotkey is empty. For Example:
Setup: Hotkey slot 1 is empty, hotkey slot 2 is not, at least one slot in the player inventory is empty.
1. Craft a stone pickaxe
2. hover over the stone pickaxe in the craft table output and push hotkey 1
Expected result: the stone pickaxe is placed in slot 1.
Actual result: the stone pick is placed in slot 1.
3. Repeat step 1
4. hover over the stone pickaxe in the craft table output and push hotkey 2
Expected result: the stone pickaxe is placed in slot 2 and the item in slot 2 is placed in and empty inventory slot.
Actual result: the stone pickaxe is NOT placed in slot 2 and the item in slot 2 remains in slot 2.
note 1: The expected behavior works as described in 1.8.9.
Note 2: The same test may be performed with any item that holds inventory (e.g. chest, craft table input, player inventory).