Puppet pins adding rough scraps

Does anyone else have a problem with Photoshop graphics having little extra image scraps after using puppet pins to distort it over time? I've tried a couple of tests and both times there were a few spots that render along with the clip to a .mov file. I don't mind it being there while working on the composition, but if it ends up on the render that sort of makes the puppet pins useless. Do I need to create an animated mask to clean up these scraps, or is there a preferred file type to use this way? I used PNG images in these.