Selection bias? Consider the type of person likely to be attracted to languages like Haskell or Clojure.
(Note, didn't read the original study so I don't know the selection criteria. Were code samples in different languages from the same programmers compared, or were there different sets of programmers per language? My comment really only applies to the latter case.)
On one hand, Haskell or Clojure probably attract more academic types who have a reputation for (consistent with my experience) on-average worse-quality code.
On other hand, the barrier-to-entry for these languages is higher so they tend to be programmed by more experienced folks. I assume that people pick functional languages in part because they believe the functional paradigm leads to higher-quality code, so the sample probably cares more about code quality to begin with.
They went to school, they where not bashed in the head with hammers.