I am new to Autos. I am on my 3rd run with them.
My first run was like yours I started them in a small pot and transplanted them after a couple of weeks. They stunted. You shouldn't really transplant Autos. Transplanting shocks a plant. With a photoperiod plant you can always catch up, an extra day or two of veg makes no difference. With an Auto you can't, you have 30 days of veg, so if you lose a few days you have lost 10% of your veg time.
So because I messed with them they stunted and I got poor results.
My next run was a great success. I mixed up some compost and well rotted manure with some Perlite in 1.5 imperial gallon pots and popped the seedlings straight in. They were then fed just tap water until they started showing pistils. Then they were fed on Tomorite tomato feed with a little added Epsom Salt until they looked like they were starting to ripen. I then reduced the concentration of the feed by 50% each week until they were done. I got 1.5oz of very nice weed from each plant, which isn't bad considering they were grown outdoors in a poly tunnel in Northern Europe.
My 3rd run of Autos have been done in the same pots, with the same medium and the same feeding regime, but this time I have employed LST. As soon as they hit 3 nodes I have been pinning them. This has made much stronger and bigger plants, with many more heads. I have vegged these outdoors and am going to finish them indoors under some COBs as the weather here has turned quickly.
My guess is that they have been shocked by the transplant and failed to recover quickly enough. Looking at the pepper plant I'd say that none of them are getting enough nutrients.
What medium are they in? What are you feeding them? What lights are you using?