diff --git a/news/hotfix.rst b/news/hotfix.rst
new file mode 100644
index 00000000..02b165e7
--- /dev/null
+++ b/news/hotfix.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Multiple morphs/targets used to break given multiple subdirectories.
+
+**Security:**
+
+* <news item>
diff --git a/src/diffpy/pdfmorph/pdfmorphapp.py b/src/diffpy/pdfmorph/pdfmorphapp.py
index 2a25a5f3..61252dee 100755
--- a/src/diffpy/pdfmorph/pdfmorphapp.py
+++ b/src/diffpy/pdfmorph/pdfmorphapp.py
@@ -487,14 +487,14 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
         parser.custom_error(save_fail_message)
 
     if opts.plot:
-        pairlist = [chain.xy_morph_out, chain.xy_target_out]
-        labels = [pargs[0], pargs[1]]  # Default is to use file names
+        pairlist = [chain.xy_target_out, chain.xy_morph_out]
+        labels = [pargs[1], pargs[0]]  # Default is to use file names
 
         # If user chooses labels
         if opts.mlabel is not None:
-            labels[0] = opts.mlabel
+            labels[1] = opts.mlabel
         if opts.tlabel is not None:
-            labels[1] = opts.tlabel
+            labels[0] = opts.tlabel
 
         # Plot extent defaults to calculation extent
         pmin = opts.pmin if opts.pmin is not None else opts.rmin
@@ -533,9 +533,12 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
 
     # Get list of files from target directory
     target_list = list(target_directory.iterdir())
+    to_remove = []
     for target in target_list:
         if target.is_dir():
-            target_list.remove(target)
+            to_remove.append(target)
+    for target in to_remove:
+        target_list.remove(target)
 
     # Do not morph morph_file against itself if it is in the same directory
     if morph_file in target_list:
@@ -678,9 +681,12 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
 
     # Get list of files from morph directory
     morph_list = list(morph_directory.iterdir())
+    to_remove = []
     for morph in morph_list:
         if morph.is_dir():
-            morph_list.remove(morph)
+            to_remove.append(morph)
+    for morph in to_remove:
+        morph_list.remove(morph)
 
     # Do not morph target_file against itself if it is in the same directory
     if target_file in morph_list:
diff --git a/tests/test_tools.py b/tests/test_tools.py
index 7bf79e13..cc891965 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -60,10 +60,16 @@ def test_nn_value(self, setup):
             pytest.approx(tools.nn_value(-value, name=None), abs(-value))
 
     def test_field_sort(self, setup):
-        sequence_files = [*os.listdir(testsequence_dir)]
+        sequence_files = [file for file in Path(testsequence_dir).iterdir()]
+        to_remove = []
+        for file in sequence_files:
+            if file.is_dir():
+                to_remove.append(file)
+        for d in to_remove:
+            sequence_files.remove(d)
         absolute_sf = []
         for file in sequence_files:
-            absolute_sf.append(os.path.join(testsequence_dir, file))
+            absolute_sf.append(Path(testsequence_dir) / file.name)
 
         # Fisher-Yates randomization
         import random
@@ -84,8 +90,8 @@ def test_field_sort(self, setup):
             sorted_sequence.append(path.name)
 
         # Temperature sort should produce same result as alphanumerical if leading character is removed
-        sequence_files.sort(key=lambda entry: entry[2:])
-        assert sequence_files == sorted_sequence
+        sequence_files.sort(key=lambda entry: entry.name[2:])
+        assert [file.name for file in sequence_files] == sorted_sequence
 
         # Check temperatures are correct
         assert fvs == [174, 180, 186, 192, 198, 204, 210]
@@ -98,7 +104,7 @@ def test_field_sort(self, setup):
 
         # Reversed sort should match alphanumerical sort
         sequence_files.sort()
-        assert sequence_files == reversed_sequence
+        assert [file.name for file in sequence_files] == reversed_sequence
 
         # Check we get the same sequence when we load header information from a serial file
         serial_file = os.path.join(testdata_dir, "testsequence_serialfile.json")
@@ -106,7 +112,7 @@ def test_field_sort(self, setup):
         metadata_sequence = []
         for path in metadata_path_sequence:
             metadata_sequence.append(path.name)
-        assert sequence_files == metadata_sequence
+        assert [file.name for file in sequence_files] == metadata_sequence
 
         # Check error thrown when field does not exist
         with pytest.raises(KeyError):
diff --git a/tests/testdata/testsequence/ignore_dir_1/ignore_1.txt b/tests/testdata/testsequence/ignore_dir_1/ignore_1.txt
new file mode 100644
index 00000000..ed6385c4
--- /dev/null
+++ b/tests/testdata/testsequence/ignore_dir_1/ignore_1.txt
@@ -0,0 +1 @@
+This directory should be ignored by PDFmorph.
diff --git a/tests/testdata/testsequence/ignore_dir_2/ignore_2.txt b/tests/testdata/testsequence/ignore_dir_2/ignore_2.txt
new file mode 100644
index 00000000..f7f3749f
--- /dev/null
+++ b/tests/testdata/testsequence/ignore_dir_2/ignore_2.txt
@@ -0,0 +1 @@
+All directories should be ignored by the multiple-morph/target command searches.