To make Civil 3D easier to understand and identify issues, Pipe Network Structures should have a warning symbol on them when the structure RIM elevation is set to match the surface elevation and the connected pipe(s) drive that elevation up.
In the screenshot below, you can see the surface elevation at the insertion point and that the structure has a reference surface assigned. However, the rim elevation is higher than the surface elevation. This is because I have a 24" pipe connected to the structure and per the structure definition with the pipe clearance requirement, it's driving the actual rim elevation up.
Only solution here is to modify the grading, lower the pipe, or change the pipe size. Regardless, a warning symbol would be helpful to identify the cause.