diff --git a/cwltool/builder.py b/cwltool/builder.py
index 4fb91efdc..9a89e903c 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -217,6 +217,9 @@ def generate_arg(self, binding):  # type: (Dict[Text,Any]) -> List[Text]
 
         prefix = binding.get("prefix")
         sep = binding.get("separate", True)
+        if prefix is None and not sep:
+            with SourceLine(binding, "separate", WorkflowException, _logger.isEnabledFor(logging.DEBUG)):
+                raise WorkflowException("'separate' option can not be specified without prefix")
 
         l = []  # type: List[Dict[Text,Text]]
         if isinstance(value, list):
diff --git a/cwltool/load_tool.py b/cwltool/load_tool.py
index a1c6dc53c..e48c19ad6 100644
--- a/cwltool/load_tool.py
+++ b/cwltool/load_tool.py
@@ -20,7 +20,7 @@
 from avro.schema import Names
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.ref_resolver import ContextType, Fetcher, Loader, file_uri
-from schema_salad.sourceline import cmap
+from schema_salad.sourceline import cmap, SourceLine
 from schema_salad.validate import ValidationException
 
 from . import process, update
@@ -124,6 +124,9 @@ def _convert_stdstreams_to_files(workflowobj):
     if isinstance(workflowobj, dict):
         if workflowobj.get('class') == 'CommandLineTool':
             for out in workflowobj.get('outputs', []):
+                if type(out) is not CommentedMap:
+                    with SourceLine(workflowobj, "outputs", ValidationException, _logger.isEnabledFor(logging.DEBUG)):
+                        raise ValidationException("Output '%s' is not a valid OutputParameter." % out)
                 for streamtype in ['stdout', 'stderr']:
                     if out.get('type') == streamtype:
                         if 'outputBinding' in out:
diff --git a/tests/test_examples.py b/tests/test_examples.py
index b63e19f92..36da186b8 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -7,6 +7,7 @@
 
 from io import StringIO
 
+from cwltool.errors import WorkflowException
 from cwltool.utils import onWindows
 
 try:
@@ -525,6 +526,20 @@ def test_lifting(self):
             echo = f.make(get_data("tests/test_bad_outputs_wf.cwl"))
             self.assertEqual(echo(inp="foo"), {"out": "foo\n"})
 
+    def test_malformed_outputs(self):
+        # check that tool validation fails if one of the outputs is not a valid CWL type
+        f = cwltool.factory.Factory()
+        with self.assertRaises(schema_salad.validate.ValidationException):
+            echo = f.make(get_data("tests/wf/malformed_outputs.cwl"))
+            echo()
+
+    def test_separate_without_prefix(self):
+        # check that setting 'separate = false' on an inputBinding without prefix fails the workflow
+        with self.assertRaises(WorkflowException):
+            f = cwltool.factory.Factory()
+            echo = f.make(get_data("tests/wf/separate_without_prefix.cwl"))
+            echo()
+
 
     def test_checker(self):
         # check that the static checker raises exception when a source type
diff --git a/tests/wf/malformed_outputs.cwl b/tests/wf/malformed_outputs.cwl
new file mode 100644
index 000000000..0fea9fb21
--- /dev/null
+++ b/tests/wf/malformed_outputs.cwl
@@ -0,0 +1,8 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+
+inputs:
+  []
+outputs:
+  -
diff --git a/tests/wf/separate_without_prefix.cwl b/tests/wf/separate_without_prefix.cwl
new file mode 100644
index 000000000..78163ddd6
--- /dev/null
+++ b/tests/wf/separate_without_prefix.cwl
@@ -0,0 +1,22 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+
+inputs:
+  src:
+    type: string
+    default:
+      string
+    inputBinding:
+      position: 1
+      separate: false
+
+stdout: output.txt
+
+outputs:
+  output:
+    type: string
+    outputBinding:
+      glob: output.txt
+      loadContents: true
+      outputEval: $(self[0].contents)