*Update*
Through lots of troubleshooting an error was found in the model.
At one of the downstream xsec the bank flow lengths were too long. Channel flow length was correct (around 185′), but the left and right bank flow lengths were wrong (around 850′).
I believe this happened when my flow lengths were off, I reassigned flow lengths in GeoHECRAS, clicked a wrong box, and this changed my overbank flow lengths.
Correcting this error corrected the model!
What I think was happening was HECRAS saw the long overbank flow lengths, interpreted a large area, and produced a slow down in the water. This therefore created a rise.