Hi,
There doesn't seem to be anything wrong with your settings. However, since you have set the parameter 'No. of culverts' to 6, it means that you have actually inserted 6 culverts at each location (all with the same geometry of 3x3m). So you need to make sure that this is correct, since it's not what you described initially.
It is however not possible to say whether the obbserved effect is correct or not without knowing the hydrodynamic conditions. If you doubt that this is realistic, I'd suggest that you try for example to refine the mesh in the channels where you have set the culverts: having only two mesh elements across these channels is maybe not detailed enough to accurately describe the flow through these channels.
Best regards,
Mathieu