Not sure, here is one possibility:
For a multiple opening, the water surface immediately upstream of each opening can vary slightly depending on the approach velocity for that opening. If it converges to a good solution, each opening should have the same energy grade line. The actual water surface is based on this energy grade minus the velocity head. The velocity head can be different for each opening.
If the energy grade for the multiple opening in your data set is consistent, I would guess that that is what is going on. If the energy grade is not consistent, it probably didn’t converge.