I've not deliberately done any retrogen in this world.Sounds like retrogen gone wrong.
My AM room is deep underground, so it shouldn't be that, and the same block twice?Did any meteors land nearby? AM2 meteors can replace blocks with stone.
Mining trees: secretly trolling you since 2013I've found it! It's my underground Mining Tree (Twilight Forest). It keeps stealing the Moonstone Blocks and exchanging them with stone.