Creator Backlash: Animator Rodolphe Guenoden said it "We're Back" was the most difficult movie he ever had to work on his entire career in animation due to it's messy production and the tight deadline keeping them from making the film better, and said that the final product reflects its turbulent creation.
Creator Killer: This was only Amblimation's second movie, but its lackluster performance helped lead to the animation house only making one more movie, Balto. By that point, Spielberg had formed DreamWorks Animation with Jeffrey Katzenberg and David Geffin, and the three men absorbed most of Amblimation's staff into DreamWorks, leaving the older label stranded.
Deleted Scene: A scene in which Screweyes cages and chains the dinosaurs, explains how he lost his eye, and blasts Brain Drain down their throats with actual cannons was fully animated, but cut from the film. Bits and pieces of it can still be found, and some frames were used in a Recursive Adaptation book.
The Other Marty: John Malkovich was originally cast as Screweyes but left due to constant script rewrites (the film's Executive Meddling also caused him to leave Hollywood and only do international productions for a few years). Kenneth Mars was chosen for the role instead.
What Could Have Been: As Stated above, John Malkovich cast as Screweyes but left due to constant script rewrites (the film's Executive Meddling also caused him to leave Hollywood and only do international productions for a few years). Kenneth Mars was chosen for the role instead.
A deleted scene has Screweyes explain his motives, and the deal with all of the crows. The ending in particular where he's swarmed and devoured by them makes a lot more sense when you learn that he fears them after one pecked out his eye as a child, and that his efforts in spreading terror are attempts to deal with his own fears.