this is something i've noticed myself, and other other champs.
my advice is to practice the shit out of it, get used to the way the spell travels.
I can't prove it but i feel like some skillshots don't actually line up how normal cast displays, or the pov/angle is awkward.
i.g. the projectile could travel slightly above or below where you mouseover, or end above or below the direction it started.
a lot of it has to do with where your champ is on your screen, whether it's nearly centered or off to the side makes a huge impact on perspective/accuracy.
all you can to is spam that spell until you know it like the tip of your... you know.
but not just with your champ in middle of screen, try it with you champ near the edge of the screen, you should notice a different feel to it.