It sounds like you feel they violated the IEP because your son is allowed under the IEP to email his assignments, apparently instead of handwriting them out. The teacher's printer is broken and she asked him to print them out and give them to her, which he didn't.
That doesn't sound like a huge violation of the IEP.
The IEP clearly states that instead of turning in the assignments that they are to be emailed to the teacher. She told him he could not email them to her. This IS a violation of the IEP.
In addition, he turned in EVERY ONE of the missing assignments. She has lost them or failed to record them in her online grade book.
The vocab tests sound like that is something your son isn't good at, which is a bummer, but that would presumably not be in the IEP.
He has dysgraphia. He will likely NEVER be better at spelling. That is why it is a learning disability with an IEP - because it hinders his success in areas he can get better in. His IEP clearly states that spelling is not to be part of the grade for him unless it is a spelling test.