MUNI doesn't even appear to be aware of the issue, or at least not until ABC 7 pointed it out. Talk about embarrassing. There are things they can do to fix it, mainly something called "shimming" or "leveling" but to do that would be a lot of work. In fact, the people who make the trains say it might be easier to fix the platforms and not the trains.
As for what happened, MUNI's not sure but thinks that whoever wrote up the blueprints has a six that looks like an 8 and oops.