You're not overreacting, especially if you're seeing a pattern of behavior and if you're the one that has to pick up the pieces. You need a better therapist that really picks apart the issue. If dad's the problem and dad doesn't understand how or why, then something needs to change: either dad's calls need to be monitored, or your son needs a post-call routine, whether that's sitting down with you to have a bowl of ice cream and dissect the call, or a favorite show you watch together, something to ease past the end of the call. (But honestly, if it's hurting your son to talk to dad, then my opinion is that you need to know what dad is saying. I'm no lawyer, so I don't know what the rules might be on listening in or recording calls so check with someone smarter than me.) But no, you're not overreacting. A mama bear's job is to mama bear.

I have the same problem my son gets violent when his dad visits usually at night he starts being aggressive with me. I told his dad about it he thinks I'm over reacting. So now he has to stay away . like tonight he had to pick up something from me I handed it to him and told him to leave my son was in the kitchen eating dinner but he knew his dad was at the door. It seems like my son thinks his dad is going to live in the home again. Trust and believe that will not happen.
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Give him lots of hugs. And positive input constantly after these calls. It will help.