I have a pcb design which has two layers with two star ground polygon pours respectively, and all the components are throughhole. When I generate gerber files however, on both layers the border of the component connects to the trace and the polygon pour. I am confused. Why is altium considering the component borders to be part of the polygon pour?
Open up the footprint associated with the parts in question.
This will allow you to click on the outline of the part. I believe that the part footprint was made incorrectly and that the outline was drawn on a physical layer.
First, select all the lines/polygons that should be on top/bottom overlay layer instead of the physical layers.
Next, change their layer to the top/bottom overlay layer.
Finally, save changes and update your pcb. Tools->update from pcb library