diff --git a/spacy/cli/project.py b/spacy/cli/project.py
index 7470e23ea..dd6b4da11 100644
--- a/spacy/cli/project.py
+++ b/spacy/cli/project.py
@@ -243,8 +243,8 @@ def project_clone(
             raise RuntimeError(f"Could not clone the repo '{repo}' into the temp dir '{tmp_dir}'.")
         with (tmp_dir / ".git" / "info" / "sparse-checkout").open("w") as f:
             f.write(name)
-        run_command(["git", "-C", tmp_dir, "fetch"])
-        run_command(["git", "-C", tmp_dir, "checkout"])
+        run_command(["git", "-C", str(tmp_dir), "fetch"])
+        run_command(["git", "-C", str(tmp_dir), "checkout"])
         shutil.move(str(tmp_dir / Path(name).name), str(project_dir))
     msg.good(f"Cloned project '{name}' from {repo}")
     for sub_dir in DIRS:
diff --git a/spacy/errors.py b/spacy/errors.py
index b3e6efdd4..c54aa804b 100644
--- a/spacy/errors.py
+++ b/spacy/errors.py
@@ -132,6 +132,7 @@ class Warnings(object):
             "are currently: da, de, el, en, id, lb, pt, ru, sr, ta, th.")
 
     # TODO: fix numbering after merging develop into master
+    W091 = ("Could not clean/remove the temp directory at {dir}.")
     W092 = ("Ignoring annotations for sentence starts, as dependency heads are set.")
     W093 = ("Could not find any data to train the {name} on. Is your "
             "input data correctly formatted ?")
diff --git a/spacy/util.py b/spacy/util.py
index 3f0a1ec6f..5be83e20f 100644
--- a/spacy/util.py
+++ b/spacy/util.py
@@ -467,7 +467,10 @@ def make_tempdir():
     """
     d = Path(tempfile.mkdtemp())
     yield d
-    shutil.rmtree(str(d))
+    try:
+        shutil.rmtree(str(d))
+    except PermissionError:
+        warnings.warn(Warnings.W091.format(dir=d))
 
 
 def get_hash(data) -> str: