Maybe he missed Ben, and Ben was just smart enough to play dead.
BTW the title of the season finale is "The Incident"
i think ben
was shot, and killed. but then later came back to life.
fast forward 27 years, he did the same thing to locke, to test to see if he was the new "island leader guy". (i.e; yet another way where ben looks like he's evil, but could likely turn out to have been the good guy all along)