Of course, there's certainly commercial permits that would not relate to any population gains. Site work also requires a permit, which happens way in advance of building construction actually happening. Furthermore, a single address can see multiple permits being pulled for different phases of construction (core and shell, tenant upfits, renovations). Thinking of some downtown retail turnover, there's been many permits that overlap with no "additional" businesses being added, just replaced. Similarly, you have residential renovations. Residential tear down and replacement on the same lot. Neither of those are gaining population.
Permits can also be issued and nothing is built due to a variety of reasons (market conditions, financing, etc).