The .net errors are typically hard to troubleshoot to know WHY exactly an error occurred. I believe in a lot of cases it has to do with how the geometry is ruled to other elements and perhaps broken as base elements are edited/copied/renamed, so those elements nullify how different elements are built. But we haven't been able to find a direct relationship to a workflow and troubleshooting these errors.
If you can post the DGN file which is having the issue, we can attempt to find the trouble element in the file which is causing the crash. In some cases you can just recreate that that geometry and reassociate any civil elements to it to "repair" the relationships.
Also, what is the exact version of InRoads you are using so we can make sure you are on the latest release of the product?
http://communities.bentley.com/products/road___site_design/f/5922/t/110086