Hello,
Negative depths, if they remain small, are not too much of a problem as mass is conserved in our algorithms. However the setting with TREATMENT OF NEGATIVE DEPTHS is more correct and ensures a mass conservation at machine accuracy (it can even be used for this if you have no dry zones). Then oscillations next to your boundary condition may reveal another problem, e.g. the fact that the flow is supercritical. If you have also dry zones in your entrance it may be the reason, try to avoid it,and also look at VELOCITY PROFILES , which with options 4 and even better, 5, may give a cleaner velocity profile at the entrance.
With best regards,
Jean-Michel Hervouet