I’ve seen this before in bridge models and it’s been caused by the ineffective stations on the downstream cross sections. If the proposed bridge has a wider opening and you keep the same flow expansion angle as you used for the existing bridge, then the downstream ineffectives get moved out, which increases the active flow area and you get a small rise downstream of the bridge where you’d think there should be no changes in a subcritical model (Q=VA).
You’ll also get a rise if the proposed channel is bigger. When you make the area bigger, the velocity goes down and thus the WSEL has to go up. I’ve never had the time to investigate and find out at what point the area gets big enough to not get a rise (and probably every site is different anyway).
Also, if the bridge is overtopping, then you often will get a rise upstream because the proposed bridge is larger (longer or greater deck thickness) and blocks more of the flow than the existing bridge did, which results in an upstream rise.