Plot hole: The premise is that the back-story is a fabrication, including the five being placed together in the police line-up and in custody in order to get them to work together. But in the flashback of Keaton in the restaurant, it is Dave Kujan who takes Keaton in. It is inconceivable that Kujan would be complicit in the staging of the line-up (and doesn't fit with the plot). And if Verbal is inventing it, then Kujan is going to know it didn't happen. It doesn't make sense and undermines the plot.
Revealing mistake: In the flashback, when the boy has his throat slit, there's no blood or wound.
Answer: Keaton doesn't believe in Keyser Soze, and is so convinced that Kobayashi is the one pulling the strings and manipulating them. They figure that if they take HIM out, they are home free.