Most creatures in D&D 5e have specifics on what attacks or weapon damage types they are resistant to. For example:
Damage Resistances: Bludgeoning, Piercing, and Slashing From Nonmagical Attacks
However, the description of the Flameskull entails resistance to piercing damange without the phrase "From Nonmagical Weapons/Attacks":
Damage Resistances: lightning, necrotic, piercing
—Flameskull, Monster Manual, pg. 134
Wouldn't that mean the Flameskull is resistant to magical piercing damage as well as non-magical piercing damage?