When Danny is woken up by the kidnapper's first call, he wakes up and the time is 3:56, but a second later when he picks up the phone the time is 3:55.
Both Mary and Danny tell conflicting stories about the first time they had sex (including Danny saying Mary raided her father's liquor cabinet), but in the season 1 finale Mary says that she was raped as a child by her father.
When Danny and James Lesure's character break in with guns drawn on the person who had lost $213,00 at the casino, and then kick the door down and find him in the bathroom, they take one look at him and say "wrong guy". But while the audience has seen the kidnapper, these two have no way to know what the kidnapper looks like. Why would they take one look at the wrong man and suddenly know he's not the kidnapper?
The kidnapper says he blames Ed because he is in charge of the entire Casino, and that he has blamed him for the last three years. But Ed wasn't in charge of the Casion three years ago, only in charge of Security. So why would a plumber have blamed the head of security, a head of security that had no run-in with him, before Ed ever managed the entire Casino?
Mary never said she was raped by her father. It was implied she was sexually abused by him but that doesn't necessarily mean she was raped. It was never stated explicitly what her father did to her.