One possibility is that the phone keeps track of the fact that "you drove 3 miles past where you were 'supposed' to stop, and then stopped at some other (specific) location."
As more and more people do that --- search the hospital, drive past it, and stop at the same specific location != the phone's predicted location --- then, statistically, we can infer that the "specific location" that everyone eventually stops at is, in fact, the location of the actual hospital.
Interestingly, this implies that the current mapping problems will eventually sort themselves out... after annoying a sufficient number of customers!
In reality Apple has been doing exactly this type of thing since iOS 4 was deployed[1], so unfortunately the privacy problems are apparently very easy to sidestep.
[1] http://www.dailytech.com/Apple+is+Tracking+its+iPhone+iPad+U...
What experience I've had with those data sources makes me unsurprised that there are misplaced businesses.
I doubt that data is being collected to help users with "more accurate maps", but probably "more accurate advertising".