When talking about code calling code "clever" typically means someone is needlessly complicated and unreadable code that (this is the accusation) serves mostly the purpose of showing off the skill of the programmer, and rhis usually means using more advanced language features. So when code is clever, people usually think it is too clever.
Sometimes code is also called clever undeservedly so. E.g. I don't think list comprehensions in python are necessarily harder to read than most for loops, but people unfamiliar with them might think of them as too clever.
