When a superflat world preset with a stronghold is entered in, Minecraft will save the preset, but without the stronghold.
How to reproduce:
Launch Minecraft, click "Singleplayer", click "Create World" and turn cheats on. Click "More World Options", click "World type - Default" click "Customize", and then click "Presets." Remove all text from the text box and enter

minecraft:bedrock,188*minecraft:stone,2*minecraft:dirt,minecraft:grass_block;minecraft:dark_forest;stronghold

Click "Use Preset", click "Done", and click "Create New World".
Enter command

/locate Stronghold

The message "Could not find that structure nearby" will appear.