Well it does have a nice green color.
I have one as well. Fruit is small too.
Let's see what others think.

Dave

For the rotted green ones, could we see a photo that shows the rotting?

As far as dwarfed fruit, I had this happen to me over the winter. I was overwintering about seven plants this year, and I decided to let two of them grow some fruit because I wanted some fresh habaneros. Then the heat in my home died. It stayed off for a while because the repair was extremely expensive. And it was cold. The peppers grew to a tiny size and then the plant went dormant. When I got the heat repaired, the plant ripened the peppers, but without making them any larger. So I had teensy, orange habaneros.

I have also seen green peppers (not on habaneros) start to rot when left on the plant during dormancy as well. There are other things that could cause the rotting on the plant (i.e., fungus). In fact, the reason dormancy could lead to this is probably because it gives fungi a chance to seize hold. But I suggest fruit-on-during-dormancy because it could explain both the dwarfing and the rotting.

I have no idea where you are from, but have your plants been exposed to any cold while setting fruit? Or been through a period of dormancy with fruit still on them? Perhaps from the weird heat/cold swings this year?

Angie

I Second the cold exposure theory. Same thing happened to mine at the end of last season.

Angie in the last picture I've attached you can see the dwarfed orange fruits and two green rotten habs, I live in South America, in Paraguay.

We have just started autumn, so the plants enjoyed full summer. Currently the temperatures are around 66F at night and 80F during the day.

I currently have three orange habs and all three have the same thing.... dwarfed fruits and or rotting. I also have a serrano, red caribbean hab and a bhut jolokia and all of them are doing great. My problem is with the habs... :-(

Based on your reply, since your other plants are doing fine, I would chalk it up to the Habanero plants being started with bad or diseased seed.

Just a shot in the dark.

Bill