The continuity error = Total Inflow - Total Outflow
The continuity error can be variable over time as this graph of the total inflow, total outflow and continuity error over time shows for the classic extran example from SWMM 3 and SWMM 4. The continuity error can be negative or positive at each saved time step and it tends to balance out over time. As you can imagine depending on how long the simulation lasts the continuity error may be much greater than zero. If you can the simulation to dry weather flow is reached in the sanitary network or the stormwater network has drained the continuity error will be better.
If we look at a bubble chart of the continuity error over time (with the bubble size the continuity error) and the y axis the Total Inflow to the network you can see how continuity error increases and then decreases over time. The white bubbles are negative continuity error points.