If I understand you correctly, the problem is that you have two ground regions but the netlist is showing just one.
You don't mention the Calibre version you are using, but check the Calibre xRC User's Guide for the section "Modeling Multiple Ground Regions." It has been available for a few years, so chances are good your version supports that. (I'm not sure if Calibre xACT offers the same feature, as PEX Ground Layer is handled differently in the two programs.)
yse, it's a problem about different ground regions, and I've tried "Multiple Ground Regions" a few times at first. But it seemed not work, so i came here for some suggestions.
And I have fixed this problem already, which is just caused by the wrong "ground layer" name~
still, many thanks!