Remember diaphragm support will fill the instrument with air whether playing loud or soft. If you play sax or clarinet choose a good reed, at the correct strength for you, and 'play it in' the day before. A breathy tone on flute. Check your embouchure. The classic 'frying tonight' wet sound on clarinet and sax.
Saliva build up behind the reed.
I have found that intonation generally improves with a pupil's all round playing experience. Most beginners however, tend to play on the flat side due to under developed embouchures. Common fault - flat in the higher register. Observe all those markings. Staccato, slurs, accents and so forth.