Edit: There's actually 1 store that isn't showing up on Apple maps, but it's also not showing on Google. It was actually a Duane Reade store that closed a few months ago and Walgreen's just replaced it. Just sent a report to Apple, let's see how long it takes to change it.
The problem has been fixed. Only 3 days later. Let this serve as a lesson that instead of complaining about a problem, you should report it to Apple and they will fix it promptly.