Practice your scales slowly. This will help your coordination and your muscle memory, as well as your breath control. See how slowly you can play a particular scale, looking at your fingers the whole time.
Keep your fingering constant. Depending on what type of fingers you have and what is most comfortable, there are several different fingerings available for some scales. Pick whichever fingering you want, but once you've decided on a fingering, don't change it for anything.
Change it up. Practicing scales the same way every day will cause you to ignore what you're playing. Try starting your scale on a note other than the tonic. Instead of playing all your scales every day, pick two or three to concentrate on for the same amount of time it would have taken you to practice all of them.
Practice with a metronome. Many saxophone players rush parts of scales because their some fingers are weaker than others. Playing with a metronome will help you isolate your weak spots and work on them.
Play scales in sections. Trills using two notes, as well as three- and five-note sections, are useful. You can also play the scale over and over starting with two notes, then adding another note each time.
Plan to practice scales every day. Make a schedule of your practice time, instead of moving from one piece or exercise to another when you feel like it. Put in at least 30 minutes of scales, and make an effort to concentrate during that time, rather than playing scales by rote.