Hello,
You need to take care about the discretization of the bathymetry when splitting your initial mesh elements. The instability in the vicinity of the downstream boundary could be caused by a bad interpolation of the bathymetry which induces unphysical water depths (or at least hard to impose).
You need to keep in mind that, oscillations near a liquid boundary, are very often synonymous of hardness in the imposition of the desired condition (prescribed elevation in your case). The probable causes are the change of the hydraulic regime, a steap gradient of elevation or of bathymetry, partial or complete drying of the boundary etc.
There is solution to dump these oscillations, which I don't recommand, and which consist on increasing the velocity diffusivity (to 10-3 or even 10-2). It is a very efficient technique, but it could hide major problems in the model.
I hope that it was helpful.
Kind regards,
Riadh Ata