There are multiple text alignment issues on Yosemite.
Pictures are worth thousands of words:
After I click on it to give focus to the text field, it awkwardly animates left, then on the last frame of the animation, the text snaps up to the proper centered position, leaving the search icon behind:
Not minding the fact that the x button is too close to the right margin, If I click on it, sometimes it doesn't work and it always makes the search field flicker.
Some more examples of bad text alignment:
1) Text in the top bar is touching the bottom title bar delimitation.
2) Text in the multiple selection boxes seems to be misaligned. I assume it's because they're not the default Cocoa widget height.