This sounds very specific to me. Please send some temporary credentials to help@bricksbuilder.io from the email address you used to purchase Bricks and also include a link to this forum thread. Then we’re happy to have a look.
I found out that this has already been reported here.
(Easier) workaround for now:
Just add a section (or whatever outer container you want to use within the popup) by clicking on the element in the left sidebar. Then you can continue working on your popup as usual.