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The reason that Spotlight works so efficiently – and so fast – is that it creates a special database called the Spotlight Index. Think of it this way: Spotlight keeps track of (it "indexes") every single word within the body of your documents as well as the file names and metadata. Each time you create, edit and save your file, Spotlight is indexing its contents and metadata.
The problem that you are having indicates that Spotlight's index is damaged and needs fixing.
The solution is to rebuild the Spotlight index, and this can be done quite easily. You start by accessing Spotlight's Preferences panel, via System Preferences > Spotlight. Then, click on the Privacy tab at the top of the panel.
Here, you can select any areas you don't want to be indexed, then run the indexer again.