core.typed fails as soon as protocols are around, no matter if typed or not.

core.clj

(ns core-typed-bug.core
  (:require [clojure.core.typed :refer :all]))

(defprotocol> ITypedTest
  (get-data [this]))

(defn> testfn :- Any
  [asdf :- Keyword, in :- ITypedTest]
  (.get-data in))

project.clj

(defproject core-typed-bug "0.1.0-SNAPSHOT"
  :description "FIXME: write description"
  :url "http://example.com/FIXME"
  :license {:name "Eclipse Public License"
            :url "http://www.eclipse.org/legal/epl-v10.html"}
  :dependencies [[org.clojure/clojure "1.6.0"]
                 [org.clojure/core.typed "0.2.44"]]
  :plugins [[lein-typed "0.3.4"]]
  :core.typed {:check [core-typed-bug.core]})