Different color cubes in one city
An outbreak only occurs due to cubes of a single color:


  If the city already has 3 cubes of this color, do not place a 4th cube. Instead, an outbreak of this disease occurs in the city (see Outbreaks below). 


And therefore a city can have up to three cubes of each color, not just three cubes overall:


  As a result of outbreaks, a city may have disease cubes of multiple colors on it; up to 3 cubes of each color. This does not affect infections.