If your complaint was framed as a request and didn't state that you already tried and failed to get a positive response from the responsible undergrad advisor, it is normal and efficient from the higher-up's perspective to send it to the person in charge.
If your complaint indeed stated that you are unsatisfied with the response from the undergrad advisor and are seeking redress, then it's normal to involve the undergrad advisor but unprofessional to forward your mail without at least masking your name. However, it would still be easy for the advisor to infer the author of the complaint, unless this is a huge department with many similar complaints coming in at the same time.
The reason why the higher-up forwarded your mail can only be guessed. Either they misunderstood your mail, thinking it wasn't a complaint but a request in line with the first paragraph, or they were unprofessional. It is within your rights, in any case, to seek redress to administrative decisions like the waiving of requisite courses, and therefore incorrect if the undergrad advisor tells you not to 'dare ask someone else'. If they don't leave it at an angry email (but I think they will), you still have the option to bring the matter to your university's ombudsperson.