Though undetected for decades, there is a penis doodle hidden in the film. It's visible in the DVD and VHS versions. At the 46:20 mark of the film, while Fievel's sister is singing Dreams to Dream, a penis doodle appear's in front of her face for one frame.
Owing to creative differences, Don Bluth parted ways with Steven Spielberg, with whom he had directed the original An American Tail (1986), as well as the first of 13 Land Before Time films. With no Bluth in sight for the sequel, Spielberg instead relied on Phil Nibbelink, a former Disney animator, and Simon Wells, the grandson of science-fiction author H.G. Wells, to direct the project.
The song "Dreams to Dream" is based on a theme used in An American Tail (1986). It is heard during Bridget's speech in the market, as well as at the end of the Orphan Alley sequence, as the camera pulls back on the orphaned mice sleeping in the rain.
One view of the cats' mousetrap (visible right before Fievel dispatches them at the end) displays a nameplate, facing upside-down, which reads "Made in Acton, London"; this was the location of the Amblimation studio where the film was produced.
Don Bluth and his animation studio, Sullivan Bluth Studios, were originally going to make the film, as they had done with An American Tail (1986). Universal agreed, under the condition that it would cost no more than $9.6 million, similar to the budget of the first film, but $3 million less than The Land Before Time (1988), which Bluth was already directing for them. Faced with the prospect of having to lay off employees at his studio, Bluth declined the job, and parted ways with Universal after finishing their commitment with "The Land Before Time." Ironically, the film was made for roughly $25 million, twice as much as "Land" had cost to make.