So I've been trying to fix my guitar intonation recently because my B string is awful. However, when guides say that the 12th fret should be the same as the harmonic on that fret, it gets a bit more difficult when that 12th fret harmonic is on the 13th fret instead. Also, the 13th fret itself is the same note as the open note. So is my guitar intonation a whole fret flat? Ive tried fastening the screws but they're as tight as they can go and it's still the 13th fret. I've seen no help anywhere for this issue and I have no idea what to do.
Sounds like your 12th fret is too low, since you need to move up the fretboard to the 13th fret to get the note you should be getting on the 12th, so you need to move the bridge saddle towards the pickups, which is the opposite of what you're doing.
You want to shorten the length of your string, and by tightening the screw you're lengthening it.
Could also be something wrong with your B string, since it sounds like that's the only one you're having trouble with.
The 12th fret is exactly half way down the string. If you are getting the octave and harmonic at 13, then you need to move the saddle forward, towards the pups and neck. Measure the 0-12 fret distance, and then measure 12 fret to saddle. they should be the same, but it sounds like your first measurement will be short, by about 1/2". B saddle on most guitars is farther back than the others, about level with that of the 6th string. Measuring is just a rough guide - it needs doing as you were, using 12th fret harmonic. Some actually check by playing 12 fret note, then fretting on 13, and plucking the string above the fretboard. It's a good guide.
Did you or someone else put a new neck on the guitar? It sounds like whoever did the replacement used the wrong scale neck. Fender types are longer than Gibson types by about one fret. This could explain the scenario you've described.
In addition to the other answers here, there's the possibility that your guitar has a zero fret- that is, a fret right after the nut, that the strings are touching. In that case, your thirteenth fret would be the octave.