See attached screenshot. There is no crash or error message and the world is still completely playable.

Yeah.... unfortunately this is a problem with my biome layout manager. Fixing this would need a rewrite of the existing biome generator, but I promise I'll get to it eventually.

Just rechecked with Ecotones 0.5.1. At least it's not on the beach, but The Pits can still form in the ocean.

Well, crap. I thought this was fixed.... I'll take another look.