Currently (Creo Parametric 3.0-6.0) one can adjust errors and warnings in Creo Parametric via Notification Center. When one tries to adjust the error messages for additional applications like Mechanism or Simulate there is no way to adjust the errors and warnings.
The lack of control leads to massive amount of error messages in Creo Simulat/Mechanism if one drives Creo Parametric part/assembly with Pro/PROGRAM or some other way using Suppress/Resume features. This is due the fact, that some of Simulate/Mechanism features will fail (as they should) due missing geometry.
At Creo Parametric 2.0 (and earlier product versions) there is no errors with failing simulation features.
Enable Notification Center settings for the Creo Simulate, Mechanism Design etc