I exported a cross-section through GeoRAS. Whenever I run a flow through the model, even if it is 0.001 cfs, some cross sections appear to be completely flooded (example below).
Do the elevations of your ‘flooded’ cross sections look correct, or does the water surface elevation appear to be too high?
How did that downstream boundary condition look? If that’s not it, maybe your model has a stability issue. Show a profile plot – with water surface and energy grade line.
Check downstream boundary conditions. It looks like backwater. Plot the profile !!! and you will see if it is a backwater caused by D/S BC or high ground at the D/S end. I understand you model a subcritical flow.