it isn't that some instruments are out of tune - it is that the "accepted" pitches for modern music have drifted from the notes are biologically and physically set by the laws of nature. Many of the "simple" instruments used especially in elementary school education are of aincient origin - and were developed speciafically because they did not require tuning.

Since the accepted values of the notes have drifted - these instruments sound "out of tune" to the modern ear.