Safari update
"“Safari.app” cannot be updated because its extensions are in use by “Spotlight.app”. Click OK and quit the application."
MacBook Pro with Retina display
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The way spotlight indexing seems to work is that the index creation process asks each Application to index the file types it "owns" and provide the indexed data to spotlight for the master Index.
On a new install or substantial update, spotlight indexing can spawn a lot of little processes to scurry around and index different types of files. They run for a while, maybe an hour or so, before everything gets completely indexed. Then they should have all quit and be happy.
It sounds like on your Mac, spotlight indexing for Safari file types is "stuck" and the process has not quit yet.
So the first thing to try is a Restart.
The next thing to try is to rebuild the spotlight index, to see if it can straighten itself out:
How to rebuild the Spotlight index on your Mac - Apple Support
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