Sometimes perfectly good peppers can have bad seeds
What you see: Dark or shriveled seeds in your pepper What it is: Seeds that didn’t properly develop Eat or Toss: You weren’t going to eat the seeds anyway, but rest assured that seeds like these are harmless and don’t indicate that anything is wrong with the rest of the pepper. Go ahead and eat it up!
Back on the farm, this pepper was busy growing into a pepper, but something wasn’t quite right in some of its seeds. It’s possible that there was a pollination snafu. Or some embryos died. Whatever it was, these little shriveled bits never quite became seeds. So, all you see in your pepper is that dried up brown speck, or maybe a seed with a dark center. They look a bit sad, but that doesn't mean that anything is wrong with the rest of the pepper.
Don't worry! This pepper isn't going to seed!