Muscle was part of animals.
Sontaran muscles were designed for load bearing rather than leverage, which could lead to unwieldiness. (TV: The Time Warrior, The Sontaran Experiment)
The Third Doctor used Houdini's trick of contracting the muscles to escape from the Eight Legs on Metebelis III. (TV: Planet of the Spiders) During his seventh incarnation, he tried to use the method again to get out of the Process's cocoon, but it was too tight. (PROSE: Cat's Cradle: Time's Crucible)
Balerium gas was a muscle neutraliser and also affected the throat, making speech difficult. The Company used it in the Consum Banks to target those guilty of fraud. (TV: The Sun Makers)
The Galapogans used the illegal muscle enhancing drug mediphosphide to help them win at the Intergalactic Trials. Their attempt to cheat was exposed by the Eleventh Doctor and the team were arrested and disqualified. (COMIC: The Intergalactic Trials)
By circa 10,000,000, human muscles were greatly reduced, as they no longer did any kind of heavy work. (PROSE: The Ark)
Bellator hoped that his final incarnation would have muscles like a Karrogian Blood-Hog. (COMIC: The Clockwise War)