That's just how it is in this game, intentionally even, I bet. You see it in the Tips, even, describing how many attacks lose their hurtboxes in their attacking limbs during certain attacks, like Mario's head for his upsmash, for example. Essentially every character has some disjoints on stronger attacks, which is why you see so much clanking where you wouldn't have seen it in past games, and why you can block some projectiles with physical attacks that don't visually appear to be disjoints (swords). I imagine this change was to level out the clear advantage characters with natural disjoints had in past games, such as sword characters and others who wielded weapons such as as King Dedede.
Regardless, this change really helps Ganondorf, since his tilts are meaty enough to be able to clank with strong attacks, such as Marth's forward tilt, instead of the past where trying such would get his foot sliced off.
