Just had a fun thing happen where a 3 slab long ship with a helm and engine that were not touching the ground turned the entire hill and the bases in it into a ship when assembled.
Pretty much screwed an entire region file, bases were now a couple cubes offset vertically, cubes were merging into each other, anything that was connected with a shaft to the bases got turned into a "ship" too and broke.
Region file had to be restored from an old backup and progression lost.

This literally what the ship looked like before assembly with a helm and motor on opposite sides there is an entire cube of empty between the ground and the slabs

This was the resulting bases after assembly

Only thing i can think of there was a diagonally cobble cube that was diagonally placed next to the ship like

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which was touching the ground... (that was used just to get on the ship...)
But the ship was on level y2 and the cube was on level y1 also