Although they have different plots, both of the male leads were raised from a young age by killers. They both have to kill people.

Both movies have a cop undercover in a prison as the main character.
The Prison takes place almost fully in a prison while The Merciless skips around a lot.
The Merciless is definitely darker but it has a really good plot that makes you never know what is going to happen next.
Both are great movies.