I traveled outside Canada once during last 3 years. It not complicated.
The flag may have come from the fact that after becoming PR in 2009, I did not come to live in Canada until 2011. I have applied for Citizenship after waiting for 3 years post 2011 move. It is simple as well to understand.
Now, the challenge would be to produce residency record for almost 3 months after I came in 2011 and was staying as guest at a relative who was also renting on cash which means no receipts. During this time, I was also searching for job and was not eligible for OHIP. The only proof that I will have is the passport stamp of arrival.