Here's what I think: I see that the rightmost menu item in your layout window is "Options". That means that you are not starting magic by reading in the sky130A.magicrc file, which would pull in the PDK with its device menus; but more importantly, it does a scaling by a factor of 2 of the database to match the DRC rules. That would make this an error in magic having to do with rounding rule distances in the GDS reading. I will have to look into the problem. However, you can avoid the problem by running
magic -rcfile <path_to>/sky130A.magicrc
, or by copying that file from the installed PDK to the local directory where you have your layout, and renaming it to
.magicrc
.