I don't have a clear idea why the connections are forming the way they are but I can offer a way to help troubleshoot the problem. Here's a link to a how-to video I made that shows some valuable techniques for finding exactly what material is on a certain net and highlighting different layers on that net one at a time. This can help provide insight. It helps us visualize the path that connectivity is taking from metal layers down through substrate or bulk or well and can help see unexpected connections between shapes.
The key part of the technique for visualizing different layers on a net starts at 1:28 in the video:
Please let us all know how it goes.