I had pepper maggots earlier this year. If you search on pepper maggots on my posts, I believe there are a few pics and some observations about the problem, from early July.
Bottom line, they destroyed about 1/3 of the pods on a handful of plants. It was gruesome, but it passed. By the time you see the maggot damage, it is too late. The flies insert the eggs through the pod skin, leaving a very small 1 to 3 mm white spot (but not a flesh puncture, just a superficial white skin puncture which is hard to see); then the eggs hatch and the maggots gorge inside the pepper; later they burrow out, leaving a hole or a few holes. By the time you see either the telltale while spot toward the stem end, or worse, a hole, it's already a done deal. You can spray the whole garden with insecticide, it won't matter; the eggs are already inside your pods.
But the thing is, at least in my case, they did not destroy every pepper. The flies pick certain pods, do their thing, and leave. Those pods are toast. If you have lots of plants, you will outlast the maggots.
I am studying up on what can be done next year to deter or pre-empt the flies from ever inserting the eggs into the pods, because that is the only way to prevent this mess.