Manaphy is based on the sea angel, which is an animal with an eerie internal glow which is similar to a firefly's (it's also a legendary, so normal rules don't necessarily apply). Xurkitree is a weird alien from another dimension so, again, normal rules don't apply.
Ampharos doesn't learn Tail Glow because the Japanese name is Firefly Light (which is why it's a Bug move). Gallade's arm blades I don't think qualify it to learn Sacred Sword in the same way that Being A Sword does for, say, Aegislash.
What is ridiculous is how Drowzee and Hypno couldn't learn...
Honestly, Yveltal should have been pure Dark or Ghost, wings or not. Xerneas being pure Fairy makes sense - it shouldn't be Ground because it's not a guardian of or representative of the Earth - that's Zygarde - but of life itself.