Harris, That doesn't sound like maggots. Maggots are pale white and don't bore into the fruit, they are laid in the outer skin of the fruit by fruit flies and dig inside.
I had massive problems with fruit fly last season. Had to get rid of most of my bigger chilli pods and lost most of my sweet peppers.
I found a fly trap that was cheap ($10AUD) that specifically attracts flies that laid eggs in fruit and kills them, and it is strong.
It states that it will attract them from 500 metres away, and it does. All my neighbours said that after i put in this single trap all they problems stopped as well.
All it is, is a clear plastic Chinese container with 2 holes cut in it and a chemical soaked cloth cable tied in the middle.
It claims it works for about 3 months rain, hale or shine. Mine has been in the garden for 5 months and it is still killing fruit fly.
Within a week of putting it up and destroying all my infected pods i never had another problem.
Another tip in early identification of infected pods is: In the lighter coloured pods you can see a tiny black mark on the fruit (you have to look hard sometimes). This is a sure sign of a puncture mark from a fruit fly.