We have addressed this to a degree by having the majority of our 'checkpoints' for application failures generate warnings rather than errors. In the results summaries when we see warnings we know those are application failures. Conversely, errors generally reflect script issues.
As an example, we use property comparisons with the MessageType set to lmWarning:
Call aqObject.CompareProperty(prop, cmpEqual, value, true, lmWarning)
Additionally, we have our own comparison routines for clipboard comparisons, CSV files, text files, etc. that all return warnings rather than errors for failures.
Not sure if that approach will work for you, but it serves us reasonably well.
