I think we found a little bug in clojure.tools.build.tasks.compile-clj/nses-in-topo. Toward the end of that function there's a line (concat ns-candidates) ;; but make sure everything is in there ... but that's done in a ->> macro and so the topo-sorted list is put after the the unsorted items. Thus the :topo sort option doesn't actually topo sort, and namespaces get loaded twice, which can cause spurious errors.