Okay, I might be wrong but I have an idea why that's happening. Skarmory gets Drill Peck as an egg move from the Spearow/Doduo lines. To get a Skarmory with Drill Peck + Whirlwind, Doduo or Spearow need to learn Whirlwind. Spearow does not get Whirlwind in RSE, but gets it as an egg move in DPP. Doduo does not at any point get Whirlwind after the Gameboy games. So I think what's going on is that the validator checks the egg moves for Spearow, sees that it gets Whirlwind as an egg move without checking to see if its from the proper generation, and then responds that Skarmory can get Drill Peck + Whirlwind from Spearow even though that isn't possible until DPP.