There are a couple of things that may be going on. Ineffective flows can reduce the amount of friction losses. Instead of the edge of the cross section contributing to the wetted perimeter/manning’s n friction, the edge of the cross section is in the ineffective flow zone. The boundary between ineffective flow and effective flow is not added to the wetted perimeter. You may want to use blocked obstructions instead.
However, even blocked obstructions can, occasionally, cause the water surface to drop. The energy grade goes up, but the velocity, and more importantly the velocity head, goes up even faster causing the water surface to drop.