It's probably because you're not exfoliating your pout first.
Here's a little trick for keeping things smooth.
What you need: A worn-out washcloth or corner of a towel. (You don't want to use anything that's baby soft.)
What you do: Run some water, and wet the cloth slightly. Rub it over your lips, in a circular motion, a few times. Then use the other corner to pat dry. Lastly swipe on your favorite color!
Why it works: The damp terry cloth gently sloughs off any dead skin, so your lipstick can go on smoother and last much longer.
How often you should do it: Like any exfoliating, about three to four times a week will keep flakes at bay. No expensive scrubs necessary.