Hey, did you win 3 times in a row or just 3 times ? It's important.
If you didn't win 3 times in a row, the guaranteed Raikou spawn option won't occur.
Also did you pick the Zap Bell for Raikou ? If yes that's fine.
You have 16,6 % for it to spawn upon defeating the Raikou Guardian each time.
Source: https://wiki.pokemonrevolution.net/index.php?title=Legendary_Beasts_(quest)#Defeat_the_Guardian