I'm having the problem where caves that come close to the surface leave this distinctive grid pattern of 1x1 holes that bore down several blocks until they break through to the caves. This happens any time I use the mod alongside mods that change the world gen, specifically Biomes O' Plenty and/or BiomeTweaker. I've tried it with just Worley Caves and either of those mods installed, and the problem was reproduced both times.

I'm experiencing the same thing using BiomeTweaker. It only happens when the topBlock is a modded block, in my trials.

forge-1.12.2-14.23.5.2768
BiomeTweaker-1.12.2-3.2.354
BiomeTweakerCore-1.12.2-1.0.39
worleycaves-1.3.0

I'm trying to build a world that is a barren wasteland and have come across an odd interaction between BiomeTweaker and WorlyCaves. When I use BT to change the topBlock to a modded block, wherever WC would have a cave break the surface, you instead get a pattern of 1 block holes.

Screenshots: https://imgur.com/a/YvkcQqg

Each hole appears where both the X- and Z-coordinates are divisible by 4, and the bottom of the hole ends on an even Y value. Going into Spectator Mode, I can see that these holes form under the surface as well, not always breaking the topBlock. This only happens when the topBlock is a modded block; modded fillers with a minecraft topBlock work just fine.

My BT script: https://pastebin.com/ptwR8JfZ

To be thorough, I've tested with multiple mod's blocks as the topBlock, and with a couple different cave generator mods (as well as vanilla) and this is the only combination where it happens.

Sorry it took so long to get back to, thank for the detailed reports.