Doc shows Matt a pistol bullet he took out of a body, and says that Indians don't carry pistols. But - and Doc would have known this - Indians carried Model 1866 and 1873 Winchester rifles, which fired the same ammunition as the Colt Peacemaker pistol, so the bullets couldn't be told apart.
The Indian guide Tobeel says that only the Henry rifle was .44 caliber, but actually the Colt civilian Peacemaker pistols and the 1866 and 1873 Winchester rifles were chambered in .44-40 (among other calibers), using a .44 caliber bullet (the 1866 Winchester was originally chambered in .44 Henry, which was the cartridge that Tobeel meant).
When Marshal Dillion has Doc weigh "the bullet", it is the bullet from the pistol not the rifles the Indians bought. Later Marshal Dillion claims the bullet weighed .44, not the typical .45. They didn't weigh the rifle bullet.