If you see the creature and perceive its spellcasting, you can counter it
Just because the spell has no visible components doesn't mean you can't see a creature casting it. Because the flameskull's spells still require verbal components, you know when it is casting a spell as long as you can hear it. If you see a creature and you know it is casting a spell, then you see it casting a spell, which satisfies the requirement for casting Counterspell.
You can only counter a spell if you perceive at least one of its components
If you were deafened, or if there was an area of silence or some other reason that you couldn't hear the verbal components of the flameskull's spellcasting, or if the flameskull casts a spell with no verbal component1, then you would be unable to perceive any components of the spell, and therefore you would not know the spell was being cast until after it took effect and it was too late to counter it.
1not possible without homebrew, since all the standard flameskull's spells have verbal component