In Chapter 11 of Story Mode, Hanzo Hasashi can be seen far off in the background fighting Kronika's forces on board one of the boats in some scenes. Hanzo died in chapter 10, and it should have instead been Scorpion that was seen fighting.
In Chapter 6, when Johnny looks at his newly-acquired scar, the reflection is of the opposite cheek.
After the young Sonya kills the young Kano, the old Kano is wiped out of the current timeline. Everyone except for the young Sonya should have forgotten that the old Kano ever existed.