Missing from the Census

Data published by Statistics Canada indicates that for the 2016 Census, the net undercoverage rate (percentage of people missed less those counted more than once) was 2.4%.  The rate has been gradually improving since 2001 when the rate was 3.1%. Undercoverage is substantially larger in the three Territories.
The CBC reported on some examples of problems with the census here. No doubt the situation was worse in earlier censuses, on top of which there's loss and illegibility of those records.