When using the SWMM calculation engine (Engine type set to "Explicit"), a high continuity error and/or hydraulic results appear to be unstable and otherwise questionable.
There are many things that can cause a high continuity error or instability with the SWMM calculation engine. First, review all your data input for errors and review the User Notification list. Errors in data entry such as elevations, including the elevations of composite outlet structures, can cause problems with the calculations which can possible impact the entire model.
Next, try reducing the "Routing Time Step" in the calculation options. Reduce it gradually until results are better. For example, you may try a routing time step of 30 seconds, 10 seconds, 5 seconds, 2 seconds, down to a minimum of 0.1 seconds for very difficult models. Smaller routing time steps are often needed in models with fast-changing conditions such as pumps that cycle and sensitive control structures (especially weirs) and flow splits.
Note that for issues related to excessive flooding or surcharging, a smaller Routing Step may not be best and a value of 5 seconds or greater may be best.
In more recent versions of SewerGEMS and CivilStorm, you can adjust addition calculation options:
Troubleshooting unstable SewerGEMS and CivilStorm results using the Implicit solver