Beware that the warning does not say that the bed level exceeds 5% of the water depth, but the bed level change exceeds 5% of the water depth. The time step is excessively large or the flow depth is excessively small for morphodynamic update. Depending on the case the message can be ignored or not. For instance, if you are interested in main channel dynamics and the warning occurs in the floodplain during a flood, you may decide that it is better to have a faster simulation with soe innacuracy in the floodplain.