Stovebolt connecting rods are long, and relatively flimsy. It's possible to twist one by simply torquing the wrist pin pinch bolt incorrectly. You might have bent or twisted a rod instead of hammering the Babbit out, but all it takes is a couple of thousandths of extra clearance to make a Babbit rod noisy. A twisted rod makes the piston rotate in the bore as it moves up and down, and causes an oddball piston slap noise.
Jerry