Do you have an example of this in action?
It’s possible that if you changed your except length to a very long length, and your post is short enough, that your after post content widget would appear on the front page.
Try something like this in custom CSS or child theme stylesheet:
.home .graphene-dynamic-widget-graphene_after_post_content {display: none;}
I may have targeted the wrong class for the widget area; you can play around with Firebug to pin down the correct one.