I’m also having this problem… additionally sometimes if you refresh the page or click checkout, it has put random things in your cart that you didn’t put there.
This started 4-5 days ago on our website and we haven’t been able to make any progress on fixing it.
UPDATE: If anyone else is having this problem this morning…
The most recent WordPress update apparently “enabled” some of their built in shipping options, which may show up as “free” options to your customers at checkout. To fix this problem, go into your shipping details and check to see what has been enabled, and disable anything that shouldn’t be used.