I am a hard and heavy user of CCleaner. I have never had any problems caused by CCleaner, which incidentally is on the MS "approved" list.
To have problems is not unusual and many are the machinations of many users, but if you seriously believe that your problems came from CCleaner, then by all means contact them. They will be more that glad to hear from you.
I use CCleaner, not to "clean" the registry but to let me know what some programs have tried to implant into my registry. I've detected malware simply by running CCleaner and Auslogic's registry cleaner.
When I remove a program, then I expect the program's uninstall feature to clean up behind itself. Most don't with Microsoft being one of the very worst offenders.