The listed outer dimensions of boxes are not always accurate to the exact CM. If you are concerned with not getting overcharged, you need to measure the final packed box and not go by the listed dimensions.
In some cases, a few CMs can make a difference in terms of volumetric weight. Next time you print a label, play around by adding or deducting a CM to each of the dimensions. Once you get to something like 41x41x41 CM, adding or subtracting a few can make a difference.
If you use calculated shipping, it's always a good idea to be slightly liberal with the measurement when you create your listing. While I am not saying human error with a sorter isn't possible, someone working at Canada Post or Fedex has no incentive to squeeze the measuring tape against the box and give you the most optimistic measurement possible. Given that this was only 2 dollars, it was likely a case where your box wasn't actually exactly 16x16x16 (41x41x41), and it might have been 42 or 43 CMs.
In a perfect world, we could squeeze the measuring tape as tightly as possible on our box and give the customer the cheapest possible rate, but the problem is that if the package gets re-assessed by someone who is going to be more liberal with the measurements and increase it by a CM or 2, we have to cover the difference, not the customer. So it's better just to take a liberal measurement in the first place assuming this is a scenario with calculated shipping or the customer asking for a quote.
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