See this newspaper story about the California legislative race in the 39th Assembly district in the San Fernando Valley portion of Los Angeles County. The incumbent Democratic Assemblyman, Raul Bocanegra, who enjoyed a 39 point lead in the June primary over his opponent Patty Lopez, lost to her in November.
California rotates names of candidates within each Assembly district. For a statewide race, that gives every candidate the top spot on the ballot in some parts of the state, and all candidates are treated equally. But for a solitary Assembly race, one candidate will enjoy the top spot throughout the district. The article explains why it appears that Bocanegra would not have lost if he had been in the top spot on the ballot. Thanks to AroundtheCapitol for the link.
UPDATE: see this story, which has evidence of ballot order affecting other same-party California races as well. Thanks to Rick Hasen for that link.