In my own defDaily commute counts as presence days in Canada. This is different. Their trip was a "long one", with stamps (i.e. proofs) on passports. I would be surprised if this isn't consider misrepresentation, although the short days are few. If you don't have stamps with 100s of daily trips to the US, then maybe the officer can understand. I don't think even withdrawing the application can solve this problem if they already figured this out. In the withdrawal form, they mentioned that they may deny the withdrawal if the file is under investigation. It's all with the officer's discretion now. A waiting game to see what they say.
Thank you for the advice. I have phoned, emailed, mailed and webformed them. I even wrote a letter by hand explaining that I discovered this mistake and would like to withdraw. Now is just to wait and see what they reply. I think I have done all I could.The physical presence check usually comes after the test. If they then find out that you have not met the requirements, then there might be repercussions because of that. The first symptom is you getting a Residency Questionnaire (RQ).
2 days short is still not meeting the requirements for citizenship.
IF they find out, then the application will likely be refused after a lengthy procedure of the aforementioned RQ submission and review.
If I were in this situation, I would let them know the mistake, apologize for the error and wait for their response. You could also withdraw the application since you know for sure you aren't eligible and apply again. Your BG checks should likely be completed soon if you apply again because your criminality and security clearances would still be valid.