I've seen this bug on my test level where I put Mobs in glass cages. (to let me see how the new textures are on them).

To reproduce it, make a glass cage 3 blocks high with only a space of 1 block in it:

• Top view : 3x3 glass with a hole at the center
• Side view : 3x4 glass with a hole of 3 blocks high at the center

Create the following Mobs with their Spawn Egg inside cage:

• Witch : Can disappear
• Ocelot : Can disappear
• Blaze : Can disappear
• Bats : Can disappear (and sometimes can pass through glass blocks)
• Cave spider : Disappear
• Villager : Can Can disappear
• Silverfish : Can disappear
• Enderman : Can disappear
• Cow : Never disappear
• Pig : Never disappear
• Sheep : Never disappear

It happens when you walk far away and come back where the cages are.
Or, it can also happen after several quit/reload the level.