For many entities, commands will output their name with the prefix of "entity.", and the suffix of ".name". So for example, "/testfor @e[type=ThrownEgg]" returns, "Found entity.ThrownEgg.name". This only occurs with some of the more technical entities, more common ones work fine. This also only occurs if the entity is left with its default name, if renamed, it works fine.

Entities this occurs with:

MinecartRideable
MinecartSpawner
MinecartFurnace
MinecartCommandBlock
MinecartTNT
ThrownEgg
ThrownEnderpearl
EyeOfEnderSignal
FireworksRocketEntity
LeashKnot
ItemFrame
WitherSkull
EnderCrystal
ThrownExpBottle

These entities have essentially the same problem, but with different prefixes/suffixes:

MinecartHopper ("container.minecart")
MinecartChest ("container.minecart")
Item ("item.[tile/block].[itemtype].[data]")

Even though hopper minecarts and storage minecarts output the same name, commands do distinguish between them correctly.