Probably because it's inaccurate/exaggerated in a couple ways.
1. Genocide refers to humans, not animals, and requires the act to be targeted at a group of people that share some sort of traits (typically race, or cultural identity).
2. Disney imported "no more than a few dozen lemmings," which doesn't really meet the numbers the word typically is used for.
Disney killed lemmings, and unless they attempted to wipe out all lemmings that share a particular cultural identity, it's probably pretty insensitive to use it in this context.
Wouldn't xenocide be a more apt description? A quick search for genocide gives the definition of:
"the deliberate killing of a large group of people, especially those of a particular ethnic group or nation."
While xenocide is described as:
xenocide (plural xenocides)
The killing of a stranger or foreigner.
(science fiction)
The genocide of an entire alien species.
(US, colloquial)
The intentional killing of an entire foreign (plant or animal) species.
Why? Genocide is by derivation the killing or wiping out of a genetic population. Why can’t that be applied to purposeful extinction of an animal species?
From White Wilderness, as the movie shows drowning Lemmings, put there by Disney employees, the narrator goes:
"And so is acted out, the legend of mass suicide and destruction of a species."
https://youtu.be/xMZlr5Gf9yY?t=2m50s