Not really bugs, but:
- Can we please get the same arrow to expand SE and user menus?
- Please vertically center the links left to the search field.
Not really bugs, but:
This has been inactive for a while, but here goes...
It seems to me that the changes you're recommending should not actually be made.
The SE and user menu arrows are fundamentally different. The SE menu arrow is a small part of the SE menu. The user menu arrow is a fully self-contained interface element (that is, clicking on the user menu arrow has a different effect from clicking on your name). For these reasons, it's better that the arrows look different, and that the arrow on the SE menu look less significant (which it does).
The links to the left of the search box, together with the search box, are specific to a particular SE site. In contrast, the one interface element on the left side--the Stack Exchange menu--applies to the whole network and its appearance and function differ only in theme, from site to site. Physically separating elements that are site-wide from those that are network-wide makes sense.
Also, if there is a space between the links and the search box, then the interface will actually feel more cluttered, because there will be just as many interface elements, but separated into more groups. There's no need to separate links like faq from the search box because they already look totally different; it's not confusing for them to be together. If we had a very large number of links, then it might make sense to move some of them to the left.
As far as I can tell, the links are vertically aligned (if that is what you meant, because the term is used differently based on context) in relation to the search box, I took a close up view and there is only as much as a pixel of difference. Even if they moved it, it would look imbalanced because of certain visual phenomena.
Why it looks like it is too far up, may be due to the visual weight and positioning of the badges, and the misalignment with the words "search", and also because of the search box having a inner shadow making it look like it is inset lower than it actually is. but if they moved the words in the search box up it would end up looking terrible for the search box.
So, it is not perfectly in line with the "StackExchange" logo, but that is not perfectly center either.
The lines for the previous picture are the same for the next:
Give them some credit, It's only a pixel off, and they are aligned with the search box it's self.