I saw this while playing around in a test world:

[10:50:54] [Server thread/WARN] [FML]: The Lost Cities loaded a new chunk (-38, 23  Dimension: 0) during chunk population, causing cascading worldgen lag. Please report this to the mod's issue tracker. This log can be disabled in the Forge config.

Version: 1.12-0.0.11beta

yes, that can still happen and is unavoidable. I have tried to minimize it but even vanilla has a few places where it will cause this. Chances are this is actually vanilla causing it (for example, the emerald ore generator is known to have this issue)