diff --git a/src/bentoml/_internal/bento/build_config.py b/src/bentoml/_internal/bento/build_config.py
index 6a55827e91c..d851751503b 100644
--- a/src/bentoml/_internal/bento/build_config.py
+++ b/src/bentoml/_internal/bento/build_config.py
@@ -679,8 +679,8 @@ def _fix_dep_urls(self, requirements_txt: str, wheels_folder: str) -> None:
                 filename = link.filename
             elif link.url.startswith("git+ssh://"):
                 # We are only able to handle SSH Git URLs
-                url, ref = link.url[4:], ""
-                if url.count("@") > 1:
+                url, ref = link.url_without_fragment[4:], ""
+                if url.count("@") > 1:  # ssh://git@owner/repo@ref
                     url, _, ref = url.rpartition("@")
                 filename = download_and_zip_git_repo(
                     url, ref, link.subdirectory_fragment, wheels_folder
diff --git a/src/bentoml/_internal/utils/__init__.py b/src/bentoml/_internal/utils/__init__.py
index 9893931710a..13e65f34992 100644
--- a/src/bentoml/_internal/utils/__init__.py
+++ b/src/bentoml/_internal/utils/__init__.py
@@ -297,7 +297,10 @@ def download_and_zip_git_repo(
             raise BentoMLException(
                 f"Failed to clone git repository {url}: {e.stderr}"
             ) from e
-        zipball = os.path.join(dst_path, subdirectory or name)
+        zipball = os.path.join(
+            dst_path,
+            name + (f"-{subdirectory.replace('/', '-')}" if subdirectory else ""),
+        )
         shutil.rmtree(os.path.join(dest_dir, ".git"), ignore_errors=True)
         source_dir = os.path.join(dest_dir, subdirectory) if subdirectory else dest_dir
         result = shutil.make_archive(zipball, "zip", source_dir)