Big Problems With Custom Fields and Comments

Here are the issues I am having right now that seem to be related.

1. I am getting duplicate custom fields with every auto save draft. (so if I am taking a long time on a post…I could have 12 of the same custom field by the end of it.)
2. When I delete a comment, it turns red and then re-appears again. A refresh of the page shows it deleted.
3. Same thing happens when I delete the custom fields. It turns red, disappears and then comes back. If you refresh the page, it is gone.

Has anyone else had this problem? I carried over in every upgrade from 2.5 up and it has done the same thing through two different themes.