@Background Pony #0F03  
It’s because they’re incorrectly focused.  
The first panel does not maintain correct eyeline (and eyesquish if the paper’s not far enough away) - a line going through center of the eye and the center of the pupil. The result is that Twilight is looking at, effectively, a spot in air just below her chin, not at the paper.  
For the second, normally there would be something they’d be focusing at in front, be it the fourth wall, the actual invisble wall of the room, some character, or whatever. But they’re drawn unfocused (or even, rather, diverging - her left eye is turned more outwards than the right), resulting in a dopey/thousand meter stare/looking into your soul expression.

A Strategic Banana Reserve would be really hard to maintain.

I swear, the eyes are nightmare inducing.