Why the file I download via GitHub API has no content?

I am using the GitHub API to fetch files from a repository. I have the functionality implemented and it does work, I download the needed files but I found something strange, out of the 4 files I get, one is empty (no content inside) even though when I go the to repository and open it there it is clearly with content. The rest of the files have their content in when downloaded. Any idea why that happens?

Here is my code:

 public int downloadFromGithub(String repo, String fileName) throws IOException {
        URL url = new URL(repo);
        HttpURLConnection connection = (HttpURLConnection) url.openConnection();
        connection.setRequestMethod("GET");
        connection.setDoInput(true);
        connection.setRequestProperty("Authorization", ****);
        connection.setRequestProperty("Accept", ****);

        if (connection.getResponseCode() == HttpURLConnection.HTTP_OK && fileName!=null) 
        {
            return saveFile(connection, fileName);
        }
        else { return connection.getResponseCode();}
}

public void downloadMultipleFilesFromGithub(String repo,String directoryPath) throws  IOException {

    URL url = new URL(repo);
    HttpURLConnection connection = (HttpURLConnection) url.openConnection();
    connection.setRequestMethod("GET");
    connection.setDoInput(true);
    connection.setRequestProperty("Authorization", *****);
    connection.setRequestProperty("Accept", "***");

    String response = getResponseBody(connection);

    try {
        JSONObject jsonObj = new JSONObject(response);
        JSONArray array = jsonObj.getJSONArray("tree");

        for (int i=0; i < array.length(); i++) {
            System.out.println(array.getJSONObject(i).get("path"));
            String path = array.getJSONObject(i).get("path").toString();
            if(path.contains("Scripts")){
               
                String fileName = path.replace(scriptsDirectoryReplace, "");
                downloadFromGithub(scriptsRepositoryDirectory+fileName,fileName);
            }
        }

    } catch (JSONException e) {
        throw new RuntimeException(e);
    }


}

public  String getResponseBody(HttpURLConnection conn) {
    BufferedReader br = null;
    StringBuilder body = null;
    String line = "";
    try {
        br = new BufferedReader(new InputStreamReader(
                conn.getInputStream()));
        body = new StringBuilder();
        while ((line = br.readLine()) != null)
            body.append(line);
        return body.toString();
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
}
public int saveFile(HttpURLConnection connection, String fileName) throws IOException {
        // opens input stream from the HTTP connection
        String saveFilePath = fileSaveDirectory + File.separator + fileName;

        // opens an output stream to save into file
        FileOutputStream writer = new FileOutputStream(saveFilePath);
        InputStream reader = connection.getInputStream();

        int bytesRead;
        byte[] buffer = new byte[4096];
        while ((bytesRead = reader.read(buffer)) != -1) {
            writer.write(buffer, 0, bytesRead);
        }
        reader.close();
        writer.close();
        return connection.getResponseCode();
}