I think most people fail to understand what code smell really is. They think code smell means bad code. A code smell is actually an indication that something else might be bad with the code. The code smell itself might not be bad.

So when a code smell appears, it means you should identify the reason it exists and potentially fix it. In this case the bad code is a buggy external library, which is difficult for you to fix. Therefore, leaving the “code smell” is the best course of action.

Your manager was in the wrong and you were right to write comments.