Why are my fees appearing twice?
This should only happen with required fees. Optional fees are not affected by this. Unfortunately, this is a problem with WooCommerce and the hook used to add fees. The error has been fixed for WooCommerce 2.1 but the release date is unknown.
If you are knowledgeable with PHP or have a developer who can help you, here is a link to the changes that were made.https://github.com/thenbrent/woocommerce/commit/8ad33260164a06a5df22c1c55ef75a41e7a2bac2