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 ...
I would do this manually. The example below was made in Illustrator, but should be possible in any vector image editor.
Create a rounded rectangle, and copy it using Ctrl+C
Add some anchors using guides to help, then select and deleted the gap segments
Finally paste the copy back in place and reduce its opacity.