I think so too. He may not come out and say it right to Amy, but I'm sure he will discuss it with Henry and Alice.

Ben and Amy have some problems awaiting them next season. Ben will always be jealous of Ricky and I think that when Ben first walked in the room, he was kinda shock to see that John was so comfortable in Ricky's arms that's why he felt that he had to kiss Amy at that very minute. And now to see that John obviously doesn't like Ben and the fact that Amy and Ricky are going to spend so much time together, that's going to cause some issues for Ben and Amy in the future lol.

Even though Ben was there more throughout the pregnancy, John knows who his father is and he probably could hear Ben telling Amy "I love you" a million times when he was in her stomach, so he probably can't stand to hear his clingy self anymore