My dad's pc has random ad pop-ups in chrome so I downloaded Malwarebytes.. and it detected 1,600 registry issues.

Can it be trusted though? I do not want to screw up his PC for obvious reasons. I remember many years ago maybe with CCleaner it screwed up my PC so bad I had to reinstall Windows....

Never had issues with Malwarebytes. CCleaner was dangerous because you could clean stuff that shouldnent be, but the spyware-cleaners mostly go by strict definitions and don't get many false positives.

Cleaning the registry probably won't remove pop ups in chrome. Pop ups are bits of javascript, whereas registry keys deal with lower level OS settings. If you don't feel confident, then you may just leave them alone, dead registry keys only really take up miniscule amounts of disk space.

Registry keys could be just PUP software that's been installed, you'd be better skimming over them to be sure of what it's wanting to remove.

On the other hand, popups on chrome would be an extension of some kind typically, uninstall all chrome extensions and delete all cache and service workers (this you'll have to do manually)

If problem persists then, dig harder through the registry keys it's found, or run AV.

Also, verify it's actually chrome your running, I've seen fake browsers install and replace chrome.exe with another in the past.

On another note:
CCCleaner will remove everything and anything it pleases which can lead to severe issues and corrupting software, unfortunately people don't look at what it's removing and just go "Eh, let's hit the button"

Actually it turned out the majority where files, not registry. Seems a lot of ads files got picked up

@pythonInRelay i still fall back to Spybot S&D when I want to clean a machine, been using that for a couple decades now I think :-p