For one, it doesn't work. Most basically, a large-scale quarantine will almost certainly trigger a mass panic. That could lead to all manner of unintended consequences ranging from vigilantism to looting.

Probably least importantly, a large-scale quarantine is a huge economic disruption. Whatever city you're quarantining effectively gets taken out of the larger economy, and it's possible that billions could be lost on top of whatever it would cost. you to just do the quarantine in the first place.