Had the same issues after upgrading woo to the last version. We had a few payment pending orders for a few days which was a bit strange. So I found this treat…
The fix. Maybe temporary but it works.
1. Install WP rollback plugin
2. In installed plugin list you will see an on option “rollback” for each plugin.
3. rollback woocommerce to 2.6.14 and it’s back to normal.
Hope this helps…
NN