Does it say anywhere that the fal'Cie themselves made Cocoon? I mean, if I made a wooden box out of planks with a hammer and nails, can you say the hammer and nails made the box, or that I did it? Likewise, maybe the fal'Cie used l'Cie to do the making itself for them, while they simply thought of the blueprints. That way, it isn't really a plothole, as the game clearly states fal'Cie uses l'Cie to do what the fal'Cie themselves can't directly do because it's against their nature. And then the fal'Cie still technically made Cocoon.

Then again, what about specific fal'Cie like Eden who serves as Cocoon's sun, or the fal'Cie who makes the food... Aargh, you're right, it doesn't make sense.