The only underground structure that can generate is Strongholds.
List of Missing Underground Structures:
Mineshafts: (can be located using the /locate command, but does not generate the structure, probably another bug of it's own)
Ancient Cities: (do not generate in a valid Deep Dark world)
Trail Ruins: (do not generate in a world that is one of their valid biomes)
Trial Chambers: (do not generate)
Would MC-241438 describe your issue?
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