So I picked this pepper today, I think it's a cayenne. Started deseeding it and halfway down the pepper I find this. Is this some sort of seed rot? Does it indicate that I did something wrong? Was it to ripe already? Can I eat it except this section of course?
We can't draw any conclusions from only one pod. Probably some fungus took hold and broke down pepper flesh which subsequently rotted before the pepper was full sized, since the dark seeds are undersized. See the Fungus Among Us topic, probably a similar situation. http://thehotpepper.com/topic/32750-mold-inside-pods-theres-a-fungus-among-us/
The pod looked and felt great. The tip was turning a darker red but near the cap just finished turning bright red. I ate the top and bottom areas which showed no signs of this problem.