Minecraft's item ID system is pretty cool, but it has some stupid stuff in it. To fill you in, when I talk about item IDs, I mean things like minecraft:stick and minecraft:stone_pressure_plate. That being said, let's get into the list:

minecraft:deadbush: The dead bush is strange, as most item IDs have each word separated by an underscore. The dead bush, however, just has the two words smacked together. Shouldn't it be minecraft:dead_bush?

minecraft:red_flower: There is literally only one flower that isn't called red flower, the yellow flower. Every single other one, even the ones that aren't red, share the same name: red flower.

minecraft:stone_slab: All half slabs in the game share the stone slab name. You'd think this would just be something like slab or half_slab but NOPE, all of them are stone!

minecraft:leaves2 and minecraft:log2: So, wood and leaves have the ID of log and leaves. However, in 1.8, acacia wood and dark oak wood was added. So, you'd think they'd share the same IDs, right? Nope! These two get completely different IDs, of leaves2 and log2. Why are these so different than the other leaves and wood?

minecraft:cooked_beef: This easily could've been minecraft:steak, but cooked beef just makes SOO much more sense!

minecraft:spawn_egg: Spawn eggs really bother me. I'll be rambling on and on with this one, so bare with me. The different spawn eggs don't have different data tags, they're all basically the same item (even though they're not). This can be seen in the creative menu with F3+F turned on. So, when I /give myself a spawn_egg, I get an egg that spawns literally nothing. This makes absolutely NO sense whatsoever. The way you're supposed to /give yourself spawn eggs is by using the EntityTag tag. But, if you try to make an Iron Golem egg (or a VillagerGolem egg), it spawns nothing! Yet, if you right click a spawner with that egg, it WILL spawn iron golems! This means you can also make spawners that spawn boats, armor stands, and minecarts! Okay, I'm done talking now.

minecraft:command_block: The thing that bothers me with this one is that the repeating command block and the chain command block have their own IDs, rather than just sharing the command_block ID but with different data tags.

And that's about it for this list! If you can think of any dumb item IDs, please comment! :D