Personally, I don't like it. It's not a pet peeve of mine. It doesn't cause a knee-jerk reaction. It's not a huge thing, by any means. I just think of all the things a person could say to another, pointing out how bad someone looks is usually not appreciated.
The message being sent might be interpreted: you look haggard; you look tired; you don't look so good; your work quality is slipping; or some semblance of the above adjectives. Whatever you interpret it to be, it's generally not going to be positive (especially if you are stressed!).
It's bad enough to be stressed out, much less to hear about how it makes you look. How about some help, instead? How about suggesting a rest? Or some other diversion? Like a caring conversation about how they are feeling...
I'm sure that most of these people don't mean anything negative by it. They're not out to rattle my cage (usually).
It's just that we're conditioned to using certain phrases from our own cultures without thinking. Yet, how many times would it be better, nicer to have something positive pop out of our mouths?