The underlying issue to me seems to be that Clojure is still not developed by a team, but by a single developer, who cannot think out of the box.
union and intersect not doing the same thing as in common lisp (accepting lists and vectors), and returning buggy values instead is just a bug, even if the developer didn't have that in mind originally, and doesn't like to support that.
You know CL doesn't have a set type, though, right? It supports lists because it has to use a different data type. This turns several O(1) set functions into O(n), however.
Also, are you sure vectors are supported in CL? Looking over Common Lisp the Language, the adjoin/member/intersection functions only mention lists.
Finally, it's not even clear CL won't return buggy values, either. From the documentation on CL's intersection function: "If either list has duplicate entries, the redundant entries may or may not appear in the result." So it's just as GIGO as Clojure.
union and intersect not doing the same thing as in common lisp (accepting lists and vectors), and returning buggy values instead is just a bug, even if the developer didn't have that in mind originally, and doesn't like to support that.