I am creating a leaf from scratch in illustrator, I made the stroke a different color than the fill, and now I can see that the stroke is sort of distorted and is not properly lined up to the actual shape itself. How can I fix this?
I guess you have drawn a separate stroke shape which doesn't fit well enough. Remove it and insert a new to the base leaf shape or (or a copy of it, no fill). Use the width tool to get some variation.
If you have a copy of the leaf shape you can even split the curve with the Scissors to get individually adjustable stroke shapes.
My basic leaf shape with no stroke
An uniform stroke is inserted
The width tool is used to get some variation. The stroke is not a separate shape in this case.