World is "regenerating" over affected terrain

Before the bug occurred, the chunks loaded and I mined them and made a home (affected them), then after a computer shut down, I loaded up the world and the terrain appeared as it was when I started. My mines were filled, and trees grew where they were before I destroyed them. Some affected things remained, such as my fences. The regeneration started at a specific chunk edge. If this bug is easily reproduced, players could constantly re-mine precious ores. Multiple world holes also appeared not far from my base. Trees and terrain are widely affected near chunk edges.

The world was supposed to remain the same as the last time I loaded it.

The world "re-generated" over affected chunks, combining original world and affected world.

Steps to Reproduce:
1: Leave Minecraft running
2: Shut down computer
3: Re-open Minecraft