Heard back from my MPs office.
She said they normally wouldn't do anything for someone within the twelve months mark. But since there seems to be confusion with the application. They can submit an inquiry.
Still worried about this potentially pissing off the immigrations office and don't know if we should move forward.
I just got the response back from my MP's office. They didn't hesitate to contact IRCC and I didn't have this issue of app being stuck in Mississauga. I just explained to them that my background check had been in progress since the end of February and that they never sent me a request for fingerprints until I prompted the VO to do so after seeing the request being made ( I think it was through Mississauga office) and the VO never followed up and it was past their due date of April 2, which is why I think my app got stalled with the background check.
It's my opinion that when they try to change the protocol on how things are done, (maybe try and speed things up, ironically) perhaps they don't follow-up with things when file transfer happens, hence the ridiculous delay in processing.