Short answer: Carlson's gun (his Luger) is not in the barn during Chapter 5 — it stays in the bunkhouse, with Carlson's belongings (his bunk).
Context: Carlson used that Luger earlier (in Chapter 3) to shoot Candy's old dog and then returned it to the bunkhouse. In Chapter 5 the action is in the barn where Lennie and Curley’s wife are; Carlson and his gun are not present there. The gun later figures in the ending (Chapter 6), when George takes Carlson’s Luger to shoot Lennie.