Whats wrong? Even if I tune all of my strings perfectly, the 12th fret of my high e string is almost a half step lower, how do I fix this?
Btw, I have a Gibson Les Paul, and tried the methods in the internet, such as adjusting the saddle but either it didn't work or I am not doing it properly.
Take it to a tech then, there might be something wrong with it. They usually take a quick look at it for free.

Try playing the 12th fret and then the harmonic above the 12th fret and see if they're in tune together.