I have looked at the previous response and clearly there is a lot to this.
Unless the court order says that you will not allowed to do with the school, then you have parental responsibility by virtue of being the mother and you have as much say in the trials schooling is the father does.
If the school are any input from you, and they are only taking the word of the father, then it’s an application to court to compel the school to take notice of what you say and ultimately, you and the father will end up in court if you can’t agree.
Although this is really important to you, it is not urgent and any court hearing could easily be a couple of months away although if there is a hearing scheduled for then, there is no reason why you could not metaphorically hijack it and in another issue.
Moving back to your initial question, it appears that the father has residence of the child and you have contact. If that’s the case, then at the end of your contact., You have to return the child in accordance with the order.
If you want something different then it’s another court application. I appreciate that your son was crying and didn’t want to return to his father and I’m sorry to say that he’s going to have to get over that until the court have decided otherwise. If there is a safeguarding issue, and provided you have proof of the safeguarding issue, then you can make an emergency application to change the current situation but you are going to need some evidence of the emotional abuse which your son is experiencing and in that respect, it would be a good idea to get social services on your side.