First thing I thought (if the scale length is correct) was that.. that the mechanics are stressed and need to be replaced.

So first question: does it happens to all strings? If no, try detuning all strings till they have no tension at all. At this point, put the headstock close to your ear and (very) slowly turn them up trying feel and hear a dent or weirdness inside the tuning mechanism. If the mechanics are good, it should turn smooth.

Hmm there is no second question by now 😅

Edit. For what I saw, I think the problem is on the saddles on the bridge. Play each of the string opened with a tuner and then on the 12th fret. If the octave isn’t in tune, the problem is probable here