I think when you save pepper seeds, you need to let the pepper get very ripe on the vine. Then cut the pepper in half lengthwise and put it on a paper plate. Let the pepper completely dry out for 2-3 weeks. Then remove the dried pepper flesh and save the seeds. Let the seeds dry a little more. Then put them in bags and you should be ok.
With a bell pepper or any pepper that has a more pronounced cone where the seeds are located, you can make a cut around the top of the pepper and all the way around the pepper. Remove the flesh and keep just the top of the pepper with the cone bearing the intact seeds and just dry out the cone with the seeds. You can probably google saving pepper seeds and someone will have a picture of this if you don't understand what I am trying to explain.
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