If you go underground, you'll see that most caves contain no Pokemon whatsoever. Pokemon only seem to be able to spawn in small, arbitrarily placed pockets of cave and nowhere else. These places are so few and far between that it's possible to get no results when using /checkspawns in some places. Large passages in mountains seem to work fine, and underground water spawns are unaffected.

In order to see the bug in action, you can follow these steps:
1- Create a world with the seed -2201234741513725254.
2- Teleport to a specific cave with /tp @p 249 20 -237. There will be a cave branch going deeper to the south of you. Don't forget night vision.
3- Observe as /checkspawns specific returns with "this is not a valid spawn location" with most of the cave, except the aforementioned branch and another spot directly west from the location you teleported to.
4- Observe as underground pokemon only spawn in the two locations and move out from there. (There is a monster spawner small distance from the location; ignore the Cubone.)
5- Go into spectator mode and observe underground water spawns in the surrounding caves but no underground Pokemon.

The only other mods I'm running are Biomes O' Plenty 13.1.0.477 and Journeymap 5.8.5p5. The world is not a Biomes O' Plenty world.

Greetings,

I have confirmed that many biomes do not have any underground spawning.