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Did I Leave These Habaneros On The Plant Too Long?

Is that even a thing?

Hello. N00b gardener here in central South Carolina. On a whim I planted some Habaneros (among other things) back in May. Despite me knowing next to nothing about gardening, I somehow kept them alive all summer. In fact the habanero plants in particular seemed to be thriving.

A bunch of them ripened up a week or so ago and I wanted to pick them but then I got busy and just didnt.

I finally had some time yesterday and want out to check them and to my horror about 8 (out of 40 or so) of them had started rotting badly. I checked the rest of the peppers and found more that had issues.

Its hard to tell but the ones in the first pic have mushy spots.

The second pic with obvious bad spots. The stem on the pepper to the right was completely brown.

The third pic looks pest related?

Thanks in advance for and insight or advice.
 

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