Thank you for your post.
Our Development and Testing departments are aware of this issue of the Popover not closing if the popover is opened by Go to Object/Field script step. I have attached your post to the original report. When any new information becomes available, I will post again.
As a workaround, use Close Popover by itself.
For additional information, if you get into this situation again where "there is no way to close it", click the Popover button and then click it again to close.