Inside iOS 6: What's wrong with Apple's new Maps
What's wrong with iOS 6 Maps: The Cloud
Outside of missing a dedicated link to Google's transit directions, the primary complaints about iOS 6 Maps seem to be aimed at Apple's servers, not the new iOS 6 Maps app itself. This includes spurious or inaccurate place labels and incorrectly located features, including being unable to find a given location by address or name.
Some of these errors are significant, while others are typos or minor quibbles related to official name changes. In the case of typos, Apple offers a way to report problems, but hides this under the location's Info tab in a "report a problem" button. For example, this Shell gas station on Market Street hasn't been there for a long time, as the dirt lot visible in Flyover indicates.
Because the "report a problem" button appears in the context of Yelp local search information, it's not readily obvious that this button is for reporting map errors rather than filing a grievance against a business or Yelp's data.
Perhaps Apple should have used the obvious "bug" icon it debuted alongside the first versions of Safari, and made the same case to new users that it did when launching the new browser: that this is a complex new product with some known issues, and that users are empowered to improve things by reporting issues they come across.
Once you know the button is there, you can report a problem with a location's information (such as its name, exact address, phone number and so on).
You can also drag the location pin to a new spot, or note that a business not longer exists, but if you just want to highlight a visual error you have to pick "my problem isn't listed" and leave a comment.