The Roommate Agreement was an important part of Sheldon (Jim Parsons) and Leonard's (Johnny Galecki) living set-up in The Big Bang Theory, but the contract wasn't always enacted, with both men guilty of breaking some of the rules over the years. Since moving in with Sheldon, Leonard had to jump several hoops just to keep his fellow physicist happy. So while the very concept of the Roommate Agreement sounded weird and sometimes borderline wrong, he mostly abided by its rules.
Written by Sheldon, fans first learned of the Roommate Agreement in The Big Bang Theory season 2, episode 6, "The Cooper-Nowitzki Theorem", then-called the Friendship Agreement. Through a flashback, it was revealed that Leonard had to agree to the contract if he wanted to move into the apartment. There was later a revision, as seen in The Big Bang Theory season 4, episode 21, "The Agreement Dissection", so as to further lean the terms and conditions to Sheldon's benefit. The Big Bang Theory never revealed the full Roommate Agreement, but since it was routinely brought up throughout the sitcom's run, fans have a good idea of what some of the conditions were.
Sheldon primarily used the Roommate Agreement to keep Leonard in line. He would hand it over his head when Leonard was doing something that he wasn't comfortable with. However, Leonard wasn't the only one prone to breaking their agreed contract. Sheldon would unknowingly do something against the agreement he drafted. However, since he's the only one who ever took it seriously, no one called him out for it.
In The Big Bang Theory season 4, episode 3, "The Jazzy Substitution," Sheldon was having a hard time coming to terms with his break-up with his not-girlfriend, Amy (Mayim Bialik). Since this was the first time that he had to process feelings for the opposite sex, he didn't know how to cope with the stress, so Sheldon decided to adopt 20 cats. This was a clear breach of contract since pets were banned in the apartment except for service animals. The situation got so bad that Leonard had to ask Mary (Laurie Metcalf) to come over and help her son.
Given how the Roommate Agreement came about, Leonard was mostly the one accused of breaking the rules. In The Big Bang Theory season 3, episode 15, Leonard was invited to observe the Large Hadron Collider at the CERN Laboratory in Switzerland, but instead of taking Sheldon with him, he decided to take Penny (Kaley Cuoco). Ultimately, he was forced to take Raj (Kunal Nayyar) since both Penny and Sheldon caught flu. Later in the same season, in episode 22, "The Staircase Implementation," Leonard insisted on turning the thermostat up by two degrees when it should always be kept at 72 degrees. This caused a massive fight, resulting in Leonard wanting to crash at Penny's unit across the hall.
The Roommate Agreement also mandated that a roommate should be informed of any impending coitus 12 hours before it takes place. Considering the many times Leonard had unplanned intercourse with various women throughout the years, this clause was broken over and over again. Sheldon wasn't exactly guilt-free either since he never announced any of his intimate moments with Amy. The gang just knew because they used to do it only once a year for the longest time. Since Leonard and Sheldon broke certain clauses of the Roommate Agreement, both of them should've had been kicked out of the apartment at different points in time in The Big Bang Theory.