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What seems to happen is that the space is kept and reused by Mongo as new data is added, so it's not necessarily a bad thing in normal use. In our testing we've been adding tens of thousands of largish entries before emptying it again, so that caused the DB to grow and grow and grow.
The same article linked above recommends running the compact command or db.repairDatabase() to rewrite and defrag all data (this blocks the database while it runs).
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