Clusterfuck is a term of US military origin, used to refer to a chaotic situation where nobody knows what is going on, nobody is in charge, and little or no progress is being made. In actual military usage, this is most often because different service branches are not adequately communicating with each other. The NATO alphabet abbreviation is Charlie Foxtrot.
Presumably, the term derives from the figurative image of an out-of-control orgy where everyone gets tangled up and nobody knows whose dick is going where. An even more fucked up situation is sometimes upgraded to a full-on mongolian clusterfuck, but that's kind of racist, I gotta say.
A very similar term, also of US military origin, is SNAFU.