Autoflowers hate being transplanted and if you did that to such a small seedling, this is really extraordinarily stressful for them. Always germinate autos in the pot they're going to finish in... But hang in there, they might be able to recover and get going but you've essentially stunted them with transplanting them. I'm a bit concerned because those pots you've got them in now don't look to be big enough for their whole lives but DON'T transplant them again - let them finish up in those pots. You'll have small plants but you should be able to get some kind of harvest...
Good luck...