The Breath of Life
While matter replication can duplicate inanimate objects from the proper blueprint, creating a living being is another issue altogether. The complexity of a living being is far beyond that of even the most complicated machine and computer; attempting to recreate a living being using a replicator almost always meets with failure.
Moral and ethical concerns about creating new life aside, only the most advanced societies have developed technology capable of mapping out something so complex as the mind of an animal. Plant life duplication is somewhat simpler, but still complex, and duplicating animal life is a task that can result in horrible deformities if not perfected.