I dunno. In this other video showing the fight with gold it shows his Mega Typhlosion (BTW the Johto starter megas look so good, you did such a good job) getting hit with Stealth Rock when the player's Blaziken came out at 4:20 after Swampert eject buttoned out. I mean I know absolutely nothing about coding, but if you plan to update this game in the future, maybe it's to do with either the move or the eject button item.Yeah, that's really weird. Good catch.
I wonder if it has anything to do with Garchomp's rough skin ability, or the Eject Pack. Maybe one of those is kind of glitched.
Reference below-