To protect your DS, you should explicitly add language to the 504 to exempt him from certain levels of misbehavior, late assignments, etc. I have found that the kids with issues tend to get in the most trouble when there is a substitute. The regular teacher, in an effort to promote better behavior with substitutes will often mete out consequences based on the substitute's report.

Otherwise, everything that you have mentioned are normal consequences in our middle school. Participation points are routinely deducted for misbehavior. For instance, one of my 6th graders lost 5 percentage points for talking during one single P.E. class such that if he is caught talking during nine P.E. classes, his grade for the quarter would be 55% and thus failing. It is also not uncommon for a teacher to grant a zero for late assignments, especially if they are more than a day or two late; furthermore, the students would still be required to turn in the assignment or risk failing altogether.

It is particularly unpleasant and difficult to navigate when a teacher has taken a dislike to your child or at least your child's behavior. You really have no choice but to bring in the 504 team to avoid a disaster.