#1
when im playing octaves like

11-13
A G

the 13 feels a bit flat but my tuner says its in tune and my intonation is perfect at 12th fret
#2
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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#4
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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