The issue is that HEC-RAS cannot have a culvert invert below the lowest elevation of the cell it is connected to. This makes sense because if the culvert invert is below the minimum cell elevation then the culvert is buried. By adding a blocked depth to the culvert you are effectively modifying what HEC-RAS sees as the lowest culvert elevation by burying the culvert.
There is not a standard way of adding blocked depths as it is all dependent on your data. I have fixed this issue by both of the ways suggested earlier in the thread, depending on the situation.
1. If I have culvert invert survey that is a touch lower than the terrain elevation I have simply added a small blocked depth so that [culvert invert + blocked depth] ≥ [terrain elevation]. For very small blocked depths it does not have a significant impact on the results.
2. If the culvert invert is significantly lower than the terrain then I have gone in and modified the terrain elevation in GIS.