https://forums.autodesk.com/t5/maya-forum/nparticles-instanc...
https://rmanwiki.pixar.com/display/RFM22/Variation+of+Instan...
Although I don't know what tool they used, probably it was something like this, where they created many instances of an object and used a random number function for the color.
Whatever they used for the seed, it must have changed between shots, program reloads, users, or something else and I would suppose the artists either didn't notice or couldn't figure out how to fix it (I suppose you would just set the colors manually on each instance)