My taxes were filed under self employed but I'm not self employed. What should I do?

Using the SE program doesn't mean anything to the IRS ... they process 1040 forms not programs. 

Now if you did not have an SE income to report on a Sch C the time to switch to a lower priced program has long passed.  You had to downgrade before you filed so it cannot be changed now.

As for the payment ... you were sent at least 3 email alerts telling you what your payment options are ...

If you chose to pay your TurboTax fees out of your Federal refund, and if your Federal refund has been delayed unusually long at the IRS (or if it's been reduced), after a certain number of days TurboTax will want to be paid.  They likely started sending you emailed bills to pay.  If you don't respond by either paying or asking for a deferment, they will ultimately debit your bank account.  If you wish to ask for a deferment, you need to do so quickly.

See this FAQ that explains the process.  The first paragraph of the FAQ has a special phone number if you have a question or have a hardship and need to ask for a deferment.  

Hours are 5AM-5 PM Pacific (8AM-8PM Eastern),  Mon-Fri.

If you need to ask for a deferment, you should call them as soon as possible.  Once they actually start the debit process, they say they can't stop it.

FAQ:  Why was my bank account auto-debited for the TurboTax fees?

https://ttlc.intuit.com/community/charges-and-fees/help/why-was-my-bank-account-auto-debited-for-tur...

The first paragraph there says:

If you’re in need of assistance, call us by the Tuesday prior to your debit date at 1-888-808-1723 to speak with a trained specialist and mention “auto-debit”, or visit TurboTax Support.