when im playing octaves like


the 13 feels a bit flat but my tuner says its in tune and my intonation is perfect at 12th fret
The human ear is not perfect and can play tricks with you. Try tuning with the 5-5-5-4-5-5 method, or with harmonics, then check it with the tuner. Chances are, your ear will have been a bit off.

Your fingers and technique also play a role in intonation, and different amounts of pressure exerted by each finger can throw off your tuning.
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yeah, your ear can also get used to you not being in tune if you've been that way for a while. There's alot of factors that can lead to you being out of tune, from technique, to intonation of frets, to many things.
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