Mushy, brown fruit with blackened seeds and white larvae inside—no external holes—points to pepper maggot or corn earworm infestation, worsened by excessive rain.
Peppers hate wet conditions. Rain depletes nutrients and promotes fungal rot. The larvae enter through the calyx (stem end) early on.
Now: Little can be done this season. Remove and destroy affected fruit.
Next year: Rotate peppers to a new bed. Feed with high-phosphorus fertilizer. Use row covers early to block egg-laying flies.
You didn't do anything wrong—weather was the main culprit.
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