In "Mayhem on a Cross" (#4.21) we learn that Sweets, like Seeley Booth, was abused as a child until he was adopted at six years old; he still has whip scars on his back. (visual scars shown to the audience). During "The Method in the Madness" (#8.5), Sweets is living in Booth and Bones's house, after having taken a bath, he was walking upstairs, with his back CLEARLY visible, and not a scar to be seen.
When Fisher walks in the house to see Bones he is carrying at least an iPad 2 but when he shows Bones the image of the bones he is holding the first model iPad which was thicker and boxier than the iPad 2.
When Sweets is interrogating Dr. Reese he states that Reese is into bondage and seeing Jessica in pain must have turned him on. As a trained psychologist Sweets would know that bondage, which is about restrain and control, is a very different fetish than masochism which is receiving sexual pleasure from inflicting pain. While there can be crossovers, most people into bondage will do what ever they can to prevent their partners from being injured or experiencing pain.
Sweets suspects that Booth wants him to keep staying with him and Brennan because Booth wants to win the office pool on how long Sweets will live with them. Booth is a recovering compulsive gambler so his participation in a betting pool should sound alarm bells for the other characters but no one reacts to it at all.
Brennan makes the statement that the list of bones that Booth hasn't broken is shorter than the list of bones he has broken. Given that there are 206 bones in the average human body, it is doubtful that Booth has, in fact, broken 104 or more of them. It is unlike Bones to make such an unqualified exaggerated statement.