I don't know what you exactly did, bit if it's true that you didn't instruct the program to fix the listed errors then there should be nothing wrong with your system after running Clean and Fix my computer.
Changes are only made after selecting all or some listed items and then clicking "Fix" to correct or delete them.
Do you have any problems when booting you system or starting your programs?
Concerning the problem with the registry health and pc health, take a look at this thread:
http://www.macecraft.com/phpBB3/viewtopic.php?f=30&t=4732#p30856