I disagree. They tracked him to Watertown and he couldn't leave because there was no way to move without attracting suspicion. The shelter in place request did exactly what was supposed to.
Evidently he wasn't bleeding enough when he exited the carjacked Mercedes for dogs to follow him, so they knew roughly where he was, but drew the cordon a little too small (he was really into soccer, probably a good runner).
So with enough surveillance, if he'd moved after daylight he might have been caught. Then again, the authorities denied themselves the use of thousands of eyeballs of Watertown subjects, who would have likely recognized him from the description (the point about blood above is that I'm assuming they assumed he wasn't bleeding heavily, a much stronger tell).
And it was one of those subject's eyeballs after they came back into play that resulted in the end of the hunt. Given what we know now, it was a mistake. Given what I'm assuming they knew then, it was not obviously one.
"it [sends a] message: if you set off bombs in a public space, we will shut down the city and hunt you like vermin until we find you."
Of course, that only works if they actually do find you, which they didn't, although they might be able to spin it that way.