I don't think the jack o' lantern eyes look very wonky. But how did you want them to look - to lie flatter (the ones in the background are raised), to sink less into the other icing (the ones in the foreground are flush with the rest of the icing), or something else? If you could describe the look you were trying to achieve, I could perhaps help. If it's simply more precise lines that you want, then use a thicker royal icing (add powdered sugar to thicken it) and/or a smaller round pastry tip or hole in a parchment cone.