How the fuck did I miss a Mudd reference? FUCK...where was it?
Sulu has a voice-over ordering the crew to prepare "the cargo vessel left aboard after the Mudd incident" for Kirk, Spock and Uhura's use to go after Khan on Kronos.
The Countdown To Darkness
comic claims that it belonged to another Mudd, but that's not part of onscreen canon and can be ignored.