Just like CCleaner, Wise Registry Cleaner can cause problems in very rare instances if you clean empty software keys. Sometimes these empty keys are needed, and if deleted then whenever you open Windows Explorer or certain software, Windows Installer will repeatedly try to install the software needing that empty key. It will try to reinstall the software and fail (because the temporary files used when installing the software have long since been deleted), and then will try again several more times until finally giving up until next temp you open Windows Explorer. Bear in mind, such cases are very rare, but I have seen them happen a number of times.
However, you can disable the check for empty software keys. All the other registry sections are safe to scan, unlike 99% of registry cleaners which will give at least occasional false positives.