Every hit in the second combo appeared to be scaled for an extra hit as well so somehow the game was counting an extra hit in the damage scaling for the entire combo. In any case, this behavior confirms that the displayed hit counter and the hit counter used to determine damage scaling are different variables so something must have caused the game to write to only one of them which suggests something unusual is going on under the hood here.
My first hypothesis is that this is probably some strange quirk with Chun-Li’s j.:h:. If it makes a stray, non-damaging hitbox, the game may have seen it “hit” and counted that hit in the damage scaling (and maybe hitstun scaling too but this combo may be tight enough that an extra hit wouldn’t let it drop). Of course, since this stray hitbox doesn’t do damage and isn’t flagged right in general (assuming it’s a buggy hitbox that isn’t supposed to be there), it may not write to everything correct it’s supposed to on hit so it doesn’t display a hit. This hypothesis could be proven wrong if circumstances were created that allowed arbitrary other moves to do this.
My second hypothesis and favored one at that is that this may involve the training mode reset feature. Was the second combo actually the first hit of the game (as in the place you were before that was character select), or was it the first hit since you used the button combo to reset training mode? If you do something like restart training mode just as you land a hit, the game may put that hit into the queue for the next combo’s damage scaling (erroneously not clearing it as everything else is cleared). That would be a pretty believable bug as well (and if it requires a frame perfect training mode restart, it would explain why it’s seldom observed) but one that would have no effect on the competitive game.
My third hypothesis is the simplest but also the least likely. This could just be a case of random hardware malfunction. This almost never happens but is possible, and if the bug is impossible to recreate, it may have to be chalked up to this. This sort of thing is really unlikely especially on a modern console, but I figured I should throw it out there.
EDIT: The CH explanation is unlikely given that I don’t think CH damage permeates through all hits of the following combo and furthermore the first combo involves the normal base damage of j.:h: whereas the second combo has reduced damage. It the stagger animations are different, it may be because of a difference in hitstun scaling.