The notes in the middle of the saxophone generally are not a problem.
It’s when you play the lowest or the highest notes that issues more often come up.
Low notes can be tough partly because they require more air and also because they will reveal any leaks that your saxophone has. These leaks will build up and affect the low notes more than other notes (if you have any leaks).
So when you practice scales, don’t just practice them in the middle of the horn. Go to the top and the bottom.
When you practice chords, go up above and down below.
Practice these areas so they sound better when you use them in your solos. And they’re going to come up in written music too.