At the site of Janko's murder, Holmes is immediately able to tell the victims were shot with 9mm and .45 caliber rounds. In reality, the caliber of a bullet cannot be determined by looking at the gunshot wound(s) or any other cursory inspection.
It was supposedly important to the shooter to not leave behind his empty cartridges as evidence - he cleaned up after himself but missed one. If it was such an important consideration to not leave the brass behind, a firearms-savvy person going into a night shooting would be using revolvers since those do not forcibly eject cartridges all over the place like semi-automatic pistols do.
When Sherlock is explaining hand-reloading to Watson and Det. Bell after finding a shell casing at the crime scene, Det. Bell comments "reusable bullets". When hand-loading 'ammunition', only the 'shell casing' is reusable. The 'bullet', or projectile, is never reused. Anyone with a reasonable knowledge of firearms, such as a seasoned police detective who carries a firearm daily, would know that.
When Sherlock explains hand-loading, Watson is completely oblivious to the concept. Someone who has been training under Sherlock for many years would certainly have been trained to recognize a large variety of ammunition. Any kind of in-depth education in firearm ammunition would cover hand-loading rounds.