In the Long Branch when Matt figures it out, Ben has his arms crossed at the table. A second later, Matt sees him holding hands with Honey.
Moss Grimmick's stable is across the street from Matt's office. This is noticeable looking through the door when Matt comes into the office. Usually, the stable is down the street. Later, when Matt and Ben are in Matt's office, Matt says he's going down to the stable to see if he can get some information about the shooting the night before. And that's what he and Ben do, they go down the street, instead of across the street.
In the last bar scene right before he gives himself up, Ben Stack is telling Honey Dare "You're my girl!". His arms are around Honey's shoulders. A cut to a close-up of Honey, the arms are gone, her shoulders are bare. Cut back to a shot with both of them, Ben's arms are back around Honey's shoulders.