Madcap theory no.1137: Ryan has some issues/addiction problems. Neil and Claire have been taking him to Sheffield for counselling or therapy sessions. Closer to home and Catherine would have been bound to find out. TLR has been having his contacts keep an eye on Ryan and has found out. He's manipulated or paid off a prison worker to falsify the records and also exerted his influence on the woman who initially reported seeing Ryan at the prison. He's doing this just to fuck with Catherine's head.
I don't think Neil is a villian. I think his own family issues have made him over-invested in Ryan, and he likes the ready-made family dynamic with Claire and Ryan.
I don't really like the idea that Becky was abused by her father or brother, that TLR didn't really rape her, or that Ryan isn't TLR's son. Catherine made it so clear in the first series that Becky was the victim of a vicious, violent rape that any change in that storyline would play into undermining tropes about rape victims.
Madcap theory no. 2382: I know that many children in abusive families live with the feeling that they will have to rescue or protect their mother. I wonder if the little girl who never takes off her coat has a knife under there? She's going around fearing that she'll have to save her mother from her father one day, but perhaps she'll end up stabbing the pharmacist or a gangster.
Will the pharmacist kill the PE teacher and his wife and then Ryan come under suspicion? I have a horrible feeling that Jo's threats to the pharmacist could lead to the whole family dying, either through poisoning or the criminal gang deciding to shut them up. Perhaps Ryan will get the blame for killing the PE teacher but an escaped TLR will take the rap for him?