I would create a PCB with connector like PCI Express.
I use a PCI Express layout and in the eeschema it appear correctly. But, if I tryu to view in 3d, the layout of my PCB are wrong; missing the board around the PCI connector.
There’s some misalignment around that circular slot to my eye. Don’t you get an error message that your courtyard isn’t a closed outline?
Run DRC and check if you got DRC violation.
In case outline do not match, 3dviewer simplifies the board outline so you may end up with something you show.
Click on the segment you want to change, two anchors should appear on two ends of the segment. Just drag and drop them to the point you’ll get small crosshair with a circle meaning these two points overlap.
Other way is to select segment, press “e” key to edit properties and enter coordinates by hand.