Fruit flies are a non issue unless you're keeping fruit in your vivarium.
Fungus gnats can find a way in regardless of initial sterility. Though I don't think a BP substrate should be wet enough for them. At least, not wet enough for them to reach pest proportions.
I think the only long term intruder in a properly set up naturalistic vivarium is the detritivore mite. Which are ubiquitous, inevitable, harmless, and probably useful.
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