Well, it may be a small annoyance, or a big one if you are a perfectionist!
Read on to see how to hack and save space. It will require a hand saw for metal, and a router.
Step 1: Using the IKEA Online Planner
After opting for doors, when placing the drawers, you may notice some unexpected spaces (marked "?!?" below), but the images are pretty small and faded, so you'll miss them easily.
The wasted space seems meaningless, but believe me, in practice, you'll notice it. The bad thing is that you cannot use that space at all.