I'm EXTREMELY unsure as to what analysis is being used to determine files that "might" need to be fixed. My brother ran this program on his laptop thinking it would help. NPE came up with winLogon.exe as something that needed to be fixed. Knowing that viruses can hide in there he clicked fix...and NPE "removed" the file. Hopefully you are aware of what happens to windows when you remove winlogon.exe and you reboot, the system doesn't work. Failure BSOD on each boot.
Luckily, I am able to fix things like this, or he would have had to take it in somewhere and pay to have it repaired. Perhaps your tool should be more informative on why its found a file and marked it to be fixed, or perhaps explain to the user what the file is for if its a windows process file.