VAC is not obligated to correct it, really. I honestly think your application was indeed processed as a TRV application as you say, because eTA applications are not accepted by paper, which is what you did.
I have a few suggestions:
1. Email the Manila VO at
MANILIMMIGRATION@international.gc.ca and mention you did not get a correct refusal letter, include a copy of the refusal you got, request for a correct refusal letter.
2. But if you want the real reasons for refusal, you can also ask for your sister's help to apply for your case notes:
https://atip-aiprp.apps.gc.ca/atip/welcome.do
3. Mention in detail your particulars for your application (bank accounts, job, if you are comfortable) so we can try to help you understand why you were refused.