When Booth is laying down pictures of the bank robbers and naming them by their code names, he ends with "Columbus", Brennan's dad. A few seconds later Russ points to the photos and identifies the top two as his mom and dad: in this shot a photo of their mom is on top, but we never saw Booth lay it down or say "Freemont", the code name for Brennan's mom.
When Booth is talking to Brennan outside of the diner and he says "He's your dad," you can clearly see that Booth's mouth moves to say the word 'dad' a few seconds after you hear him say it.