you have to add and namespaces with (gen-class) forms to the :aot key in your leiningen project file. Next you have make sure you do a `lein compile` to actually generate the class

core.clj

(ns lein-maybe-bug.core
  (:import leinmaybebug.SomeClass))

(gen-class :name lein-maybe-bug.SomeGenClass
           :prefix "somegenclass-")

(defn somegenclass-test [this]
  (SomeClass.))

project.clj

(defproject lein-maybe-bug "1.0.0-SNAPSHOT"
  :description "demostrates some odd leiningen behaviour with java sources and gen-class forms"
  :source-path "src/clj"
  :java-source-path "src/jvm"
  :javac-options {:debug "true" :fork "true"}
  :dependencies [[org.clojure/clojure "1.3.0"]]
  :aot [lein-maybe-bug.core])