I think the problem comes from transplanting... you say you damaged the roots and it's most likely this has affected their ability to support the plant's growth and photosynthesis.
Autoflowers should always be planted in the pot they're going to spend their whole life in... transplanting them is highly stressful and dangerous as you've found out by damaging the root system. This accident may well spell the end of the plant's ability to produce much of anything - autoflowers have a certain schedule for when things happen and it's not something that can be manipulated like it can be when growing photoperiods. All of that being said, however, your plant looks basically healthy .... I wouldn't worry too much about those first leaves as they will die off anyway. Continue on and treat her gently... You can give her some root enhancers to help her develop more roots and in a week or two you can start giving her nutes but at 1/4-1/2 strength. By week 4, she should be going into pre-flower but if you don't see that until week 5, I wouldn't be concerned. Cross your fingers she'll have time to recover from the stress of transplanting and give you a great harvest!
Good luck!