When checking for consistency errors, it's usually helpful to skip reference lists. That's because hyphenation, capitalization and spelling of titles in reference lists should match the actual titles (which may be different to the preferred style for that document).
PerfectIt automatically scans for reference lists and, where it finds them, will not include matches in those lists as possible errors. If for any reason you do want to include possible consistency errors in reference lists, click 'Sections to Skip' in the PerfectIt toolbar or ribbon, then untick the box to skip references.
Automatically locating the reference list in a document is not always accurate, so you can set PerfectIt to skip a section with one of these methods.