In Season 1, Tommy's wife Janet asks his brother Johnny how "Jenny" and the kids are. But in Season 3, when his then ex-wife does appears, her name is "Angie".
In Season 1, Tommy's Father states he is 72-years-old and can take care of himself. But in Season 3, at his birthday party he is turning 83.
Towards the end of season 3 when Tommy confronts Johnny's killer, he mentions that Johnny was 41. Johnny is later called Tommy's little brother. However, since Tommy and Janet met in high school and had a child then (Colleen) who in season 4 is 18, that would put Tommy and Janet both in their mid-30's.
Every ghost Tommy talks to throughout the series is as they were when they died except for his son Connor, who died as a young boy but whose somehow a young adult in the afterlife.
In Season 2, when Tommy is supposed to be working at a firehouse on Staten Island, the Engine number is 3xx. House on Staten Island are 1xx. 3xx would be located in Queens.
In the Season 1 episode DNA, while Sheila and Tommy were at dinner, Sheila's wine glass fills up immediately after she drains it completely just seconds earlier.
No New Yorker would ever leave his truck unlocked, as Tommy always does, especially after his theft recovered Escalade was returned.
Early in the series, Tommy owned two adjoining houses which Janet managed to sell without Tommy's signature. Later on she mentions that she's broke and what happened to the money is never explained.