Maybe? I'm speculating here as it's not my field. The obvious explanation to me is very different to the obvious explanation to every other comment I've seen so far. That difference seemed interesting enough to be worth posting.

The question of where liability falls after a repair isn't covered in the articles linked unfortunately. It seems plausible that it was initially whoever wrote the software and is now someone else.

I think it's extremely likely that this disable-train-on-various-conditions behaviour is exactly as specified and documented since train software is a bit obsessed with formal methods and documentation. It's then only "silent sabotage" to the extent that said docs were ignored.

It's credible that a way to easily disable these safety checks for the case where it's now someone else's liability wasn't considered worth paying for by whoever bought the train. It's tomorrow's problem after all. Also the customer may not be totally convinced of the necessity of the software dev paranoia, especially if they're not liable for failures.

So sure, maybe this is evil/negligent software people at the train company. I don't see that conclusion well supported by the article.