Did you enable debug? If you didn't then it is already disabled. You would know how to disable it if you enabled it so i am guessing that as you are asking how to disable it, it is not down to being debug being turned on.
If you get a error on a page, check the edits for the mod. If debug is disabled and there is an error showing then the only way to stop users seeing it is fixing what is causing the problem.
It might resort in more errors. If mods aren't really compatible with the auto installer it may mess up. If the mod is badly written anyway, the mod will still show errors or not work properly.
Nothing is perfect... As phpBB3 develops, some of the find lines won't be exactly the same as the previous version. For humans we can shorted the search line and find the new line of code (which is usually only slightly different). The auto installer will not be able to find the line and just give up as it won't work out where it is supposed to go.
Quite often when you install mods correctly anyway they still don't work 100% as the author makes a mistake or it causes problems with another mod you have installed.