From what I've checked on the eggs being shiny, the first pokemon I bred in Battle Resort was Charmander (from a charizard and ditto) and it turned out shiny. After Charmander, all other pkmn hatched, aside from charmander, through the same method is no longer shiny.
Then I tried to breed again in Route 117, this time Blastoise and Ditto, and i hatched a shiny squirtle, after that, aside from squirtle, no other shiny.
Conclusion: maybe there's a part that in the code that save the value of the first pokemom bred in either place and so the only pkmn shiny hatched is those bred first using shiny code?