I have had to have nails backed out and re-nailed because the JHA wanted to make sure the area was nailed.
The inspectors that have never built a home do not understand that it is not always the framer not knowing where to nail or how to nail in a straight line.
Some reasons why they may miss sometimes.
Wood is not always straight, even in engineered trusses.
Plywood/OSB not straight,
Trusses bent while installing because of the lifting from the crane, even wind
Walls not straight, plumb or out of square
When possible they should be removed, and for the most part(now) they are. This is near impossible on a re-roof, so get over it.
The biggest issue was framers moving from hammers to nail guns. There was a lack of training and a learning curve. This is one reason why there are wind mits now.
Understanding how we got where we are now goes a long way to understanding the building codes and wind mits. They do heed each other but the do not correlate.