Like bouncybunny said, Lisa tells Dean that Ben isn't his. But, the similarities are just too much. Everyone in the fandom basically agrees that Ben is Dean's son. And then of course, something really really sad happens later on in a much later season... I can't tell あなた anything, but it has to do with Dean and Ben and Lisa.
Near the start of season 3, Dean visits his ex Lisa while working on a case near where she lives, and learns she has a son now. The boy's age and similarities between Ben and Dean make Dean suspect he could be the father. He starts liking the idea. But at the end of the episode, Lisa tells Dean that she had a paternity test done and that some trucker she slept with after Dean was the father. She also realises that Dean seems disappointed at this, so I doubt she'd lie to protect Ben from rejection. I guess there could have still been a mix up with the test, though.
Lisa and the writers say that Ben isn't Dean's, but a majority of the fandom just ignores what they say and are convinced otherwise. Like me. I say that Ben is Dean's. To be true, whatever the characters and writers and actors say about the show, あなた don't have to believe it. あなた can believe what あなた want about the show.
