This is something I accidentally discovered and it doesn't look like it can be patched (not on the PS2 at least). By holding L2 and using the direction pad, you can control the direction you want the ball to bounce.

Say you don't want the ball to bounce into the endzone for a touchback, you'd hold L2 and press UP on the directional pad. The ball will bounce and leave it in a bad field position for the receiving team.