OP, well done for coming on here to ask advice.
Being released from prison is scary and when you have been imagining how lovely it will be to be back with your family, and then it turns out not to be so lovely, it's easy to get frustrated.
Try and see your child's point of view:
This bloke turns up who she is expected to love and obey. She doesn't love you (yet) in the same way as she loves her mother. Mum has been there for her without fail. She will be wondering (subconsciously probably) whether you are staying for good or not.
You sleep (I assume) in the marital bed. A place a safety for many children when try are sick, sad or upset at night. Suddenly you are there, and not (yet) a trusted person.
She now shares her mother's day to day affection with you. She is no longer the complete focus for her mum. You are there with needs, rights, demands.
She is figuring it out, quite apart from working out normal 3 year old things (like finding out how far she can push her limits). Obedience and Respect are not appropriate expectations for a 3 year old.
Try to be patient and kind. Above all, speak with your wife and find a joint approach.
Good luck, it is clear you care and want to get it right.