If you create a biome-group that contains oceans, then that ocean won't spawn any isle biomes. Oceans that do spawn through land-rarity are not affected.

Config:
Biomegroup (Ocean, 0, 100, Ocean)
Landrarity: 99
Land Size: 0
Land Fuzzy: 3
Deep Ocean isle size: 6
Deep Ocean isle rarity: 98

This also occurs whenever you generate a world where a biome-group's land rarity is less than 100.

Config:
Biomegroup (Land, 2, 80, -any biomes-)
Land Rarity: 99
Land Size: 0
Land Fuzzy: 3
Deep Ocean isle size: 6
Deep Ocean isle rarity: 98

The reason why I would use biome-groups for oceans in the first place is that it is much more precise than using land rarity alone.

Edit: Made the post a bit more clearer

I was previously using ocean size 1. When I changed it to 0, the result still remained the same. Certain parts of the ocean spawned without isle biomes. I also added in some of the values of my configs. I believe that will be enough to reproduce this bug. If it isn't enough i could show more values or my entire config.

There must be a difference between the oceans spawned by the biome group and the oceans spawned because there is no biome group.

TerrainControl has its size variable inverted: higher size numbers give smaller biomes. If you try to spawn a bigger biome (low size number) inside a smaller biome (high size number), it simply won't spawn, without telling you why.

Make sure the biome group that contains the ocean biome has a size of 0: BiomeGroup(OceanGroup, 0, rarity, names). Alternatively, increase the BiomeSizeWhenIsle of the Deep Ocean biome to make it fit in smaller oceans.

If it still doesn't work, then there must be something else preventing the isle biomes from spawning, but without seeing your configs I wouldn't know why.

@rutgerkok confirmed for latest version