I had originally set up a payment plan but then paid in full. I was charged still even though I already paid. How do I stop future payments/ get refunded?

You will need to contact the IRS and speak with an agent to get the payments stopped and the additional payment refunded.

Call the IRS: 1-800-829-1040 hours 7 AM - 7 PM local time Monday-Friday
When calling the IRS do NOT choose the first option re: "Refund", or it will send you to an automated phone line.
So after first choosing your language, then do NOT choose Option 1 (refund info). Choose option 2 for "personal income tax" instead.
Then press 1 for "form, tax history, or payment".
Then press 3 "for all other questions."
Then press 2 "for all other questions."

Or you can contact your local IRS office. See this IRS website for local IRS offices - http://www.irs.gov/uac/Contact-Your-Local-IRS-Office-1 or call 1-844-545-5640 to set up an appointment