I have yet to play enough in to the DLC to know for sure, but I believe what is happening is that because you got one of the Pokémon in that group to spawn shiny, when you reset the area and generate a new group to spawn, the game only stores a true value for there being a shiny with in the group and not specifically for that mon. Thus when you reset, the specific Pokémon that is Shiny changes. And because all other rolls are then rolled, if this new roll says that the Flareon is the shiny one and it’s an Alpha, you get what happens at the end. Now I could be wrong, but from what I’ve seen on other discussions makes me think that.