MC 1.12.2
forge 2532
Waystones_1.12.1-4.0.17
waystone wrongly generated over existed structures, braking and sredding houses, half-buried in the ground, sometimes several in one village

4 simultaneously in one village on screenshot

I also have this issue. MC 1.12.2, Forge 14.23.0.2500 Waystones 1.12.1-4.0.17. This has been an ongoing issue in 1.12.1, haven't used the mod before that.