If you look at the Safari traffic light icons, the spacing above them is narrower than the spacing below. It's a bit hard to see immediately but it's highlighted with red lines in that section.
And the arrows aren't vertically aligned with the buttons. I don't despair, it's common of Apple to make big changes and gradually improve over time, Aqua wasn't perfect, but in Mountain Lion (despite not being truly Aqua, it has evolved to a certain perfection.) – what Apple have released in Yosemite is for developers, it will surely change before the open summer beta, and it will surely change again before Golden Master.
Top aligned with the arrows? Weird choice, if it is a choice at all and not coincidence. If it is on purpose, I would like to see a version with larger traffic lights that also align with the bottom of the arrows. Those might be too large, but I would want to see them, anyways.
