As Paddy and his gunman are leaving Maura's house, the gunman shuts the door as they're leaving, you can clearly hear the door shut but when Jane shows up and is cutting the ties off Maura's and Tommy's hands and feet, the door is wide open as if it was never shut.
Isles tells the union rep at the dock that male and female muscles are identical and that the only difference is the size of the skeletal frame. Male musculature is 30-50% denser due to testosterone induced hypertrophy.
Maura tells Rizzoli that Bobby Fischer is a world chess champion. Bobby Fischer was a world chess champion (1972-75) who died in 2008, three years before the episode aired.
Maura wants to keep the fact that Paddy Doyle is her biological father kept quiet, but both she and Jane talk openly about it while at the docks surrounded by dock workers and other police officers.
Maura questions aloud to Jane, Tommy's strategy of moving his rook to B5. But when the IM texts on Maura's laptop are shown, it says "Rook to B8".
When Rizzoli was about to watch the video of Ray, she speculated that Paddy (Doyle) and Ritchie were working together; she meant Paddy and Ray.