Originally filed as an issue for function scan-all, which at the time I was unaware was deprecated in 0.3.0 alphas. I have tested against the newer scan-dirs as well, and it has the same problem.
When there are both .clj and .cljc files defining the same namespace, tools.namespace scan-dirs and scan-all can use the dependencies from the .cljc file, ignoring those in the .clj file, whereas for Clojure/Java the opposite should be done.
See sample project and its README here for steps to reproduce: https://github.com/jafingerhut/tnstest
Note that Clojure/Java's behavior is to prefer .clj file over a .cljc file defining the same namespace, even if the .clj file is in a directory that is later in the classpath than a .cljc file. According to Alex Miller email on clojure-dev Google group, this behavior is by design. Link: https://groups.google.com/d/msg/clojure-dev/d5Hb1E7zfHE/sPybIAxgCwAJ
tools.namespace 0.2.11 and 0.3.0-alpha2