What irks me most about Minecraft is the fact that every SMP multiplayer server I try to play on is a lag-filled piece of crap with artificial borders on the world and a lot of the modpack items banned due to various "cheating" issues. I'm sick of it, and sick of having to go back to lonely SSP worlds where there's nobody to interact with.
Related to that, the vast number of servers that are so loaded down with plugins, automatic chat spam asking for donations, random prizes and things, etc., that it ruins the feel of the game. Usually you can find one or two good, small servers (usually whitelisted) where people are friendly and cooperative with each other, and the owners tend to be very lasseiz-faire - these are quite enjoyable to play on if you can find one (let me know if you do).
Things that irk me:
Just about everything that's been done with vanilla mobs since beta (Dinnerbone...), except maybe bats.
Having an odd number of wooden planks.
People spelling quartz with an 's'.
Lots of mods add things that greatly outclass railways as a mode of transportion. I really like trains, and would like to see them used more often.
Clay being hard to get in large amounts. Really, in vanilla it's only a building material...
Boat controls being broken for no good reason. Seriously, did no one try the controls out before releasing them?
While I'm on the subject, boats are apparently made of tissue paper.
Intermediate crafting steps. I'll put up with them a little, but some mods overdo it way too much.
Mods that eat diamonds like no tomorrow, for no good reason.