Make sure to save the document before running a test on it.
Select only a couple of tests at a time, unless you have a very small document. Getting a huge list of potential issues often takes longer time to manage.
Use the Options dialog box to uncheck tests that you aren't interested in, or tests that result in lots of false positives.
Some tests only make sense in certain scope. For example, tonality needs to be checked for scores only, while page layout needs to be checked for parts as well.
An issue marked as “error” doesn't necessarily mean an error, if the “issue” is intentional.
If Run only Safe Tests is turned OFF in the options, make sure to not switch to any other program on the computer during the scan.
Use
View HTML to view all currently reported issues in your web browser. The tables in that view will also display the details side-by-side with the issue.
Don't replace a machine scan with a manual check of the material. Use it as an additional tool.