I've noticed this too when audibling between formations EA Sports originally intended for "4-3" defenses and formations intended for "3-4" defenses. The way each position on the field is indexed relative to one another across different formations doesn't match up, which is causing players to reposition themselves in a way which is visually jarring and in some cases actively disruptive to playing sound football.
Again, the entire way Madden handles defensive playbooks needs an actual do-over.