Users can botch program input in more ways than you could ever imagine. To detect an error, check JSAPResult.success() after parsing the command line. It will return false if there were any problems.
Once you detect a problem, you have a number of options:
Display program usage (see HelloWorld_5 example)
Display help information (see HelloWorld_6 example)
Display messages specific to the user's errors (see HelloWorld_7 example)
Obtain a list of parameter IDs for the problematic items through JSAPResult.getBadParameterIDIterator(). Then obtain the individual exceptions for each ID through JSAPResult.getExceptionIterator(String id) and related methods. After that, you're on your own.
Any combination of the above.
If you have used SimpleJSAP error handling is largely simplified, as it will be handled automatically. Remember just to call messagePrinted() after parsing and take appropriate action.