That doesn't explain why they didn't add this when migrating to the Clipper card, but I feel like "nobody thought to change it" or "we wanted to reduce risk by not introducing changes while migrating" seem like more likely explanations than malice.
Also, Clipper cards have been around many years. They aren't a recent addition to BART.
by taking money from those weaker than it, since it is a large well financed organization and the people riding it will not be equipped to fight it (legally), that's malicious.
Having worked in, for, and around governments, this was almost certainly an oversight that hasn’t been a big enough of a fire in comparison to the other fires.
Making a public stink about it makes it a bigger fire though, so the system is working as intended!
Assuming a value system in which certain acts are wrong even if not observed / punished, some acts can be rational _and_ malicious.
(This isn't intended to say anything either way about BART's actions here, which are obviously not the same as literal robbery; I'm mainly disputing the idea that rational acts can't be malicious.)