edit: more stuff:
Clint's gun from The Good, The Bad, and the Ugly is an 1851 Colt Navy, a .36 caliber cap and ball. No one has ever made a .36 caliber cartridge, to my knowledge.
There were metallic cartridges during the Civil War (.44 Henry Rimfire, .22 Short and .56-56 Spencer and a couple more) The legal ability to convert an 1851 Colt Navy to the Richards-Mason cartridge conversion didn't happen until 1871. Why?
1871 is when the breech loader patent held by Smith and Wesson ran out.
Yes, it is entirely possible someone could spend a boatload of money at the time and have a gun illegally converted by a gunsmith.
Also, for more errors, look at Lee Van Cleef's belt - you will see metallic cartridges in the loops, even though there are percussion caps on the cylinder of his revolver.
Plus, the gatling gun shown in the film was used in combat for the first time during Petersburg, in the middle of June, 1864, and even that was considered a demonstration. It was accepted into the Army in 1866, after the war ended. The battle of Glorietta Pass, around which this movie happens, occured out west where no Gatling gun ever appeared, in March of 1862.
Leone made a western set against a Civil War backdrop. Some things are just going to be anachronisms.