A violation was the act of breaking a rule or law.

In 2259 of the alternate reality, James T. Kirk recorded a log on Delta Vega in which he stated, "Acting Captain Spock has marooned me on Delta Vega, what I believe to be a violation of security protocol forty-nine point oh nine, covering the treatment of prisoners aboard a starship." (Star Trek)

In 2366, the USS Enterprise-D, upon entering the Romulan Neutral Zone, was in direct violation of the Neutral Zone. (TNG: "The Defector")