Don't put child in the middle of a parenting conflict with your ex-spouse
Bruises spark fears of abuse

I don't know how long you have been separated or divorced, but it sounds like communication and trust are not on the table and there seems to be a lot of fear about the father's parenting abilities.
The best way to protect your child is to develop a healthy and businesslike communication with the father.
Can you put yourself in his position for five minutes? If your son showed up during the father's access time with a big bruise and said that he couldn't remember how he got it, what do you think the father would think and should do?
If you can keep your communication businesslike, sticking to the facts and asking for clarification instead of making accusations, you are more likely to be able to start building a new way of relating to each other.
Remember, your son is learning from the two of you how to deal with conflict. Why not call the father and ask whether he noticed the bruises and whether he knows where your son might have got them?