I note that the reaction above is quite lukewarm. Perhaps because it is only really visible/painful when the logo is blown up larger than it is usually seen. But for the current round of community ads, an ad was made precisely by blowing up the Math.SE logo.
I am posting to meta.SE because I looked and found a number of sites whose logos look similarly "off" to me. I also hope that by making this post, the community ads for which SE staff will provide a graphic for, will not use the logo that is on the front page (pretty much the only part of the website with the logo.) (source on math.meta call for community ads: "staff will generate a frame for the ad with this site's theme, for brand consistency")
The same persists on their meta sites. I was not systematically searching, so I guess I missed some; 3,5,6 are less obvious, but 1,2,4 are visible when smaller too.
I don't understand why, but Math.SE has a sprite sheet with the correct logo (link to math.meta post). Perhaps it is the same with the other sites, and this can be used to fix it easily without say, calling in a designer (and maybe even all at once).