I've lived in San Francisco more than 20 years at this point. Some things get better, some things get worse, but overall I'd say it's about the same. I used to work a couple blocks from there, and I just ran past it on Sunday, and the neighborhood was always kinda sketchy. And just a couple of blocks away is a pleasant, upscale grocery store, Harvest Urban Market, that has done just fine.
So I suspect this is something more about Whole Foods than any surprising change. E.g., did the pandemic and the resulting drop in the downtown population in the area put a whole in the store's profitability?