One way to confirm that that your model structure is correct is to use SimBiology sbioconsmoiety function to identify conserved moieties. You can read more about it here. If you haven't already, you will want to explicitly add species to your model to explicitly track any eliminated species.
If you suspect that your errors are due to integration tolerance issues, you might also try changing settings related to absolute tolerance scaling (which is described in more detail here). Specifically, I would first try turning off automatic scaling, and next try turning it back on and adjusting the value of AbsoluteToleranceStepSize. While this automatic scaling feature helps for most models, when it does cause problems it tends to be due to early time steps when a species starts out at 0 and changes extremely rapidly. Decreasing the time scale of this step size can help SimBiology better determine the magnitude of such rapid changes.
-Arthur
