Earlier quoted context omitted.
Until recently, BART used magstripe tickets where all information was stored on the ticket itself. It might not have been possible to implement a time window with that. 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.
I wouldn't call it malice. It's simply a rational decision. BART makes more money with the fee than without, so absent political pressure to discontinue it why would they? 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.