I found a rift between stone bricks on top of a battle tower. An entity passing through gave me this every time until I managed to put a door down.
(Additionally, don't know if I'm doing it wrong, but wood and iron dimensional doors seem to be a bit wonky when placing on top of rifts, and rift particles stay even after the remover works)

crash-2018-07-07_13.45.02-server.txt

Don't know if this is important, but the door also stopped the tower from generating past its y-value.

Yeah, we should really check for other worldgen structures before generating ours one of these days.
(Wonky how? Particles die out very slowly, but they should disappear eventually.)

The issue isn't the worldgen. It's that entities passing through a natural rift without a door crashes the game. This can result in a world being lost due to an entity always being inside a frame.
As for the wonky bit, the wood door didn't work placing from either side of the rift. The iron door worked one out of four times on a specific side.
Particles die out, but end up frozen in midair and not disappearing, even when the rift has closed.

The TileEntity of that block is not what it is supposed to be as a result of a worldgen conflict. That is why it is crashing.

Yeah, all of these might be good things to sort out in the near future.