When the player punches a minecart (entity) to gain its item. the item is named entity.MinecartRideable.name
Related issues
Comments

Can confirm.

Breaking various things yields different results.
Minecart (Plain): entity.MinecartRideable.name
Minecart w/ Chest: container.minecart
Minecart w/ Furnace: entity.MinecartFurnace.name
Minecart w/ TNT: entity.MinecartTNT.name
Minecart w/ Hopper: container.minecart
All of these have the same id:"" tag, but their tag:{display:{name:""}} tag is screwed up. Crafting and placing and other things are not affected, so it seems to be purely graphical. (Minecarts don't stack, so that can't be screwed up.)

Can confirm for 1.9-pre1.

Can confirm for 1.9-pre2.

And Minecart w/ Command block: entity.MinecartCommandBlock.name

Please change the title of the bug from
Destroyed and picked up destroyed changes name changes to "entity.MinecartRideable.name"
to
Destroyed and picked up minecart changes name to "entity.MinecartRideable.name"

Confirmed for 1.9 pre-release 4

Confirmed for 1.9 final release.
yup, can reproduce