Last year Microsoft denied that they blacklisted Registry Cleaner CCleaner on Microsoft Answers, saying:
CCleaner is not in any Microsoft Blacklist and there are no Blacklists regarding other domains in the official Microsoft forums
Today Microsoft is no longer as reticent, and has officially marked CCleaner as a Potentially Unwanted Application on their Microsoft Security site:
Microsoft did not explain why it made the decision, but the company has never been a fan of registry cleaners.
CCleaner has in the past been compromised to deliver malware to Windows PCs, but this is some years ago, and a bit long to hold a grudge. There have also been some issues with CCleaner not being compatible with Windows 10, though those issues have now been fixed.
In general, however, CCleaner provides features which are already built into Windows 10 and is somewhat redundant in this day and age. Nevertheless, the company will probably not be happy with Microsoft taking such direct action against it.