As others have said, factory build guitars are made within tolerances but sometimes exceed limits.
Correct tuning of your guitars is a multifactorial problem.
When you fret at the 12th you make the string longer and hence increase the pitch slightly. The higher the strings sit over the fretboard, the more they are elongated when fretted and the sharper the pitch. If all of the strings are playing sharp at 12 the first thing I would look to reduce is the nut and bridge heights.
If they are good then check the break angle on the nut, should be set for strings to come off the very edge.
If all the strings are sharp at 12th then your saddle is in the wrong place and needs moving backwards, buy a new one and start over. When you move the break point on the saddle backwards be aware that all the notes will drop, not just at the 12th fret.
Spend some time making a map of the sharp/flat errors at each fret. It could even be that all of your frets are fab except the 12th which needs filing backwards.
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