Edit:
You may be missing a legendary that is seen in some combat, here is a list of them
https://forums.pokemmo.com/index.php?/topic/133673-completing-the-pokédex-legendary-pokémon/
There are things that require having the complete pokedex, to complete it you dont need any legendary since there are only 7 obtainable permanent and 6 temporary, over time there will be more
It will be by probability, if when breeding you touch where it says the minimum and maximum IVs (15-30 and 25-28) you will see what probability each one has