I wouldn't say W3C screwed up. IE6 was using border-box and switched to content-box eventually in IE7. The other browsers were all using content-box back then and W3C standards embraced content-box. When IE7 came along, they flipped to content-box, but it doesn't provide a box-sizing CSS property which became essential 5 years later (IE7 is released in 2006). As Paul mentioned, it does seem more intuitive to have it border-box after all. It is hard for W3C to envision this is going to be the way people prefer things so many years ago too; I'm just glad there's a box-sizing attribute to give more options to developers.
Side note, IE6 is border-box by default. IE7 changed it to follow W3C standards eventually. Perhaps one of those times IE got it right. They're quite the hipster it appears. ;)
My major annoyance. I always panic when I see that message. I have an odd habit of saving right after I open my files now.