If a structure that cannot generate in a biome does generate in that biome due to superflat world generation, /locate cannot locate that structure.

How to reproduce:

1. Click Create New World, choose Superflat world type, click Customize and select the "Overworld" superflat preset.
2. Change the preset's biome to one that doesn't have villages (e.g. ocean, forest)
3. Create the world.
4. Find a village by flying around in Creative mode.
5. Try 

   /locate village