Coin nerds study the real ones in excruciating detail - to the point that people catalog not only the various dies that were used to strike various coins but the states of those dies (i.e. Early die state == pristine coins. Middle die state == a crack or chip might have started to form which presents as a raised line or spot on the surface of struck coins. Late die state == chunks of the die might be missing.). This is often done through reverse engineering -- examining enough examples of struck coins to identify differences in the the dies used. The dies themselves can be identified through unique markers -- a polish line here, the exact positioning of a letter, a microscopic defect, etc.
So when you are able to identify the known dies, a counterfeit will stick out like a sore thumb. And if it was made from a cast copy of a known-good coin, then those will have their own telltale giveaways.
In short: The counterfeits will always have subtle differences.