Your organization likely did something unconventional with the registry that made systems break when touched by CCleaner (perhaps a groupware tool, or perhaps the broken systems had already been FUBAR'd by intrusive software and CCleaner's attempt to fix that FUBAR triple-FUBAR'd it).

That doesn't mean CCleaner's behavior is correct, but it's probably a situation the developers haven't been able to test against. For what it's worth, I've run CCleaner's registry cleaner on dozens of machines and never had a problem of any type, and I still use CCleaner sometimes because it's a simple way to clean the temp/junk files left by many common applications with one button click.

I always feel a little nervous when I run the registry cleaner, and while I haven't noticed any problems, I also haven't noticed a meaningful improvement after running it either. I should probably stop doing it just for that reason.