I think they originated by me copying and pasting the rounded square, I need them gone. 
They are telling you that the edges aren’t breaking the larger surface into inner and outer regions. You can try selecting all of the faces and running Intersect Faces. If that doesn’t work, try tracing a single edge segment with the Line tool.
It could also be telling you that those edges aren’t on the larger face and are instead floating off it slightly. If that’s the case, you’ll need to move the edges onto the larger face.
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Thanks, I’ve fixed it now. I selected one square that had some bold lines, and dragged it by the upper middle part of the line to all the other rounded squares. 
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