Random errors with terrain generation

[the-lenoz]

Sometimes I'm getting malformed terrain in obj files - some pieces of it are not in right place but just flat and located with zero elevation. I use Constraint elevation calculator and NaturalNeighbor interpolator. I tried to know why does it occur but I got strange behavior - one osm data file renders into different obj files on different devices with same config.
Here is osm data downloaded from openstreetmap.org rendered on laptop with debian:

And here is the same data but rendered on server with ubuntu:

I attach an archive with all data:
link