This notification is identifying an Open Shape set to Fill, so this is a different issue that will need to be addressed. What is shown if you select ‘Show me’ button?
As for inverting the QR Code output. I simply selected the QR Code, then add an outward Offset of 0.5mm to it on the same fill layer.
One of the little squares the QR generator spit out isn’t closed? That’s interesting. Sounds like a question for Oz & co.
Can you close it and carry on?
Turn the Offset from both inside and outside to only outside and a small amount. You should get one outline produced. You can practice with a simple square to see what I am showing. I have the resulting Offset shapes set to red to see easier.