When Abby is explaining to Gibbs that the serial number has been removed from the Glock pistol, the serial number is visible on the pistol.
When the school bus pulls up in front of Stephen Rose's house, neither the yellow or red lights are seen blinking.
As Gibbs' life flashes before his eyes, a temporary grave marker for Shannon Gibbs is seen. It is dated February 29, 1991. Since 1991 was not a leap year, there would have been no February 29.
In the alternate reality where Kate survived, the doctor told Tony he had a boy; later, Abby says that Kate and Tony had a baby girl named Kelly named after Gibbs daughter. However, these are two different alternate realities. In the first reality where Kate survived, and is seen, Gibbs has still killed his family's murderer. Only later, when Kate's baby is discussed in the basement, is the reality in which he did not avenge their death explored. Given the episode's theme of "ripples in a pond" making countless changes down the road, it is perfectly reasonable to believe the difference in Kate's child's sex was intended.
In the diner scene when Gibbs is being served by his mother she motions to fill his coffee cup. The cup is already visibly full and through she makes the motions of pouring she does not tilt the pot enough for the coffee to come out.