diff --git a/src/flake8/checker.py b/src/flake8/checker.py
index a454f2f..5482454 100644
--- a/src/flake8/checker.py
+++ b/src/flake8/checker.py
@@ -86,6 +86,7 @@ class Manager(object):
         self.options = style_guide.options
         self.checks = checker_plugins
         self.jobs = self._job_count()
+        self._all_checkers = []  # type: List[FileChecker]
         self.checkers = []  # type: List[FileChecker]
         self.statistics = {
             "files": 0,
@@ -234,17 +235,15 @@ class Manager(object):
             ) or is_stdin
 
         checks = self.checks.to_dictionary()
-        checkers = (
+        self._all_checkers = [
             FileChecker(filename, checks, self.options)
             for argument in paths
             for filename in utils.filenames_from(
                 argument, self.is_path_excluded
             )
             if should_create_file_checker(filename, argument)
-        )
-        self.checkers = [
-            checker for checker in checkers if checker.should_process
         ]
+        self.checkers = [c for c in self._all_checkers if c.should_process]
         LOG.info("Checking %d files", len(self.checkers))
 
     def report(self):
@@ -260,7 +259,7 @@ class Manager(object):
             tuple(int, int)
         """
         results_reported = results_found = 0
-        for checker in self.checkers:
+        for checker in self._all_checkers:
             results = sorted(
                 checker.results, key=lambda tup: (tup[1], tup[2])
             )
diff --git a/tests/integration/test_checker.py b/tests/integration/test_checker.py
index 0c14474..93cc239 100644
--- a/tests/integration/test_checker.py
+++ b/tests/integration/test_checker.py
@@ -216,7 +216,7 @@ def test_report_order(results, expected_order):
     # Create a placeholder manager without arguments or plugins
     # Just add one custom file checker which just provides the results
     manager = checker.Manager(style_guide, [], [])
-    manager.checkers = [file_checker]
+    manager.checkers = manager._all_checkers = [file_checker]
 
     # _handle_results is the first place which gets the sorted result
     # Should something non-private be mocked instead?
diff --git a/tests/integration/test_main.py b/tests/integration/test_main.py
index 42ad76c..9424e99 100644
--- a/tests/integration/test_main.py
+++ b/tests/integration/test_main.py
@@ -195,3 +195,12 @@ ignore = F401
     py_file.write_text(u"import os\n")
 
     _call_main(["--isolated", "--config", str(config), str(py_file)], retv=1)
+
+
+def test_file_not_found(tmpdir, capsys):
+    """Ensure that a not-found file / directory is an error."""
+    with tmpdir.as_cwd():
+        _call_main(["i-do-not-exist"], retv=1)
+    out, err = capsys.readouterr()
+    assert out.startswith("i-do-not-exist:0:1: E902")
+    assert err == ""