So far I have only gotten this to happen with igloos, but I have not tested all of the structures so there may be more. To reproduce:

1. Load up a new world in single player with cheats enabled and the attached datapack. It will give you an advancement whenever you enter an igloo.
2. Use /locate to find an igloo and enter it. You should get the advancement as normal.
3. Exit the igloo and save and quit. 
4. Reload the world. Use /advancement to revoke the igloo advancement (will be named "test:igloo_enter")
5. Enter the igloo again. You will not receive the advancement this time. Instead, change your gamemode to Creative and fly to Y=90, with the igloo X and Z coordinates. Once you go to Y=90, the advancement should be granted like it did before.

I'm not sure if the Y=90 bounding box shift happens for other structures that may have this bug (if any). Attached are screenshots showing the advancement being given before the reload and then at Y=90 after the reload.