When Hank looks up to the hay loft and sees Cale's leg sticking out, it is obvious that Cale is lying face down. When Hank prods Cale with the rake handle to wake him, Cale sits up from a face up position.
Matt talks about the two bullets Doc Adams removes from Cale's shoulder and says that one was a pistol bullet and one was a rifle bullet. Cale had been shot once by Mr. Archer using a Winchester model 1873 and once by Sterret using a Colt style pistol. Both weapons used the same .45 ammunition so there would be no noticeable difference between the slugs.
Cale is shot twice, but after Doc removes the two bullets, there is no blood on Cale's undershirt, and no bullet hole.
When Doc removes the bullets from Cale, he doesn't remove Cale's undershirt. The operation would have been easier without the shirt in the way, and more sanitary. This is a common occurrence throughout the series.