To check your simulation accuracy, run the simulation over a reasonable time span. Then, either reduce the relative tolerance to 1e-4 (the default is 1e-3) or reduce the absolute tolerance and run it again. Compare the results of both simulations. If the results are not significantly different, you can feel confident that the solution has converged.
If the simulation results do not appear to be accurate,
For a model that has states whose values approach zero, if the absolute tolerance parameter is too large, the simulation takes too few steps around areas of near-zero state values. Reduce this parameter value or adjust it for individual states in the Integrator dialog box.
If reducing the absolute tolerances does not sufficiently improve the accuracy, reduce the size of the relative tolerance parameter to reduce the acceptable error and force smaller step sizes and more steps.
Certain modeling constructs can also produce unexpected or inaccurate simulation results.
A Source block that inherits its sample time can produce different simulation results if, for example, the sample times of the downstream blocks are modified (see How Propagation Affects Inherited Sample Times.
A Derivative block found in an algebraic loop can result in a loss in solver accuracy.