Hi Toby,
When the water depth gets very low, you might get very high velocity on the shallow areas, with the high velocity (it exerts high shear stress on the bed), you might encounter instability in solving sediment advection-diffusion equation. But I'm not sure if it is your problem...
In my model, I use
TIDAL FLATS = YES
OPTION FOR THE TREATMENT OF TIDAL FLATS = 1
TREATMENT OF NEGATIVE DEPTHS = 2
MINIMAL VALUE FOR DEPTH = 0.1
to deal with tidal flats. The MINIMAL VALUE FOR DEPTH = 0.1 ensures the location where the water depth is below 0.1m could get corrections.
As suggested by Schmirre, I also use THRESHOLD FOR SEDIMENT FLUX CORRECTION ON TIDAL FLATS = 0.1. So it means no erosion happening when the water depth is below 0.1m.
If you put the outfall sources in the model, I remember I read it somewhere, they should not be on the bottom plane since the bottom plane is imposed as boundary conditions. In your case, indeed it can cause such problem.
I don't know how to tackle this problem at this moment. Did you include TREATMENT OF TIDAL FLATS? Maybe try the OPTION FOR THE TREATMENT OF TIDAL FLATS = 2? This will remove the dry locations from the computational domain, but I'm not sure if it will help...