Merge Pencil Line Deformation

Hey all,

I have a piece of a puppet drawn out using the poly line and ellipse tool, when I go to “merge pencil lines”, the vector path of the drawing becomes warped. This has occurred for a few of the elements I’ve done for the character so far. As far as I’ve been able to determine, all of the anchor points match up to one another when this occurs.

I have no idea if this is a factor, but I’ve needed to use the Contour Editor tool to delete a few of the stray anchor points that the Cutter tool hasn’t been able to pick up properly.

Any help in figuring out why the vector paths aren’t retaining their shapes would be appreciated.

Image is attached to show the before (top) and after (bottom)