What you're observing is probably the lack of a strong line on the left side. The right edge of the Y Combinator logo ought to form a guide line down the page, with the voting arrows' right edge X pixels to the left and the text X pixels to the right of that, and this line should also propagate through the text entry box and the reply button and so on. Instead, there's the logo, the link, the textbox and reply button (which do at least line up with each other), and the first layer of comments, each of which has its own individual vertical line. (I think. Comments and the title text are close but I'm not sure it's quite right, and there's so much interference in between it doesn't matter.) I Am Not A Designer but I know enough to know that's wrong.
Also, the bottom of the Y in the logo should form a horizontal line that the rest of the text in the title bar lines up with, whether or not that happens for you appears to depend on the zoom level of your browser. (For me right now the "Add Comment" is visibly above the Y, but when I zoomed in to look closer it actually dropped below that line. By the way, designing on the web is hard. Also my website sucks and I know it. It's on the list.) Something should probably also be done with the horizontal line the voting arrows line up on.
Cleaning that stuff up would be a start. It probably wouldn't be enough, and then I'd be stuck, because I only get the really basic mechanical stuff. Everything I've phrased as fact in this comment should be taken to be opinion, it would just be very tiresome for me to type and you to read the same caveat over and over.
What you're observing is probably the lack of a strong line on the left side. The right edge of the Y Combinator logo ought to form a guide line down the page, with the voting arrows' right edge X pixels to the left and the text X pixels to the right of that, and this line should also propagate through the text entry box and the reply button and so on. Instead, there's the logo, the link, the textbox and reply button (which do at least line up with each other), and the first layer of comments, each of which has its own individual vertical line. (I think. Comments and the title text are close but I'm not sure it's quite right, and there's so much interference in between it doesn't matter.) I Am Not A Designer but I know enough to know that's wrong.
Also, the bottom of the Y in the logo should form a horizontal line that the rest of the text in the title bar lines up with, whether or not that happens for you appears to depend on the zoom level of your browser. (For me right now the "Add Comment" is visibly above the Y, but when I zoomed in to look closer it actually dropped below that line. By the way, designing on the web is hard. Also my website sucks and I know it. It's on the list.) Something should probably also be done with the horizontal line the voting arrows line up on.
Cleaning that stuff up would be a start. It probably wouldn't be enough, and then I'd be stuck, because I only get the really basic mechanical stuff. Everything I've phrased as fact in this comment should be taken to be opinion, it would just be very tiresome for me to type and you to read the same caveat over and over.