Without seeing your files and knowing the details, here are a few things I'd check:
1. If you know the hydrodynamics, validate it first.
2. Upstream and downstream BCs are accurately specified
3. Bed composition is accurately specified (including size and fraction of different sediment classes; spatial variation of sediment)
4. Mesh quality (maybe try refining your mesh and time steps if the actions above have been checked)
These are just a few things I can think of that are most likely the issue on the top of my head (and I'm not a very experienced user), but I hope it helps.
Best,
Jason