If you have trains in a blueprint, the orientation for those landfill tiles does not respect the orientation of the trains, and instead always prints vertically.
My suggestion would be to simply ignore trains during the calculation, as they would be placed on rails anyhow, which get their own landfill. Unlike most things, you can actually place train ghosts on water. They do not seem to check for water collision at all, and thus should be able to be safely ignored.
