This might be an issue with the initial conditions. Let’s assume that there are no lateral inflows to the reach that you are modeling. Therefore, the simulation should start with a situation in which the inflow equals the outflow and that condition is maintained for the travel time thru the reach. Suspect that the downstream boundary condition and the initial flows do not match – and the model is trying to adjust while the inflow hydrograph is occurring. To check this possibility, use some warm-up time steps and attach a constant flow equal to the initial flow to the beginning of the imposed upstream hydrograph.