UPDATE: From Safari v. 10.0 this annoyance is fixed. Search bars are now located in the top-right corner of the viewport. Yay \o/. Original entry below.
A search-box in OS X applications is almost always found at the top-right of the viewport. But Safari does its own thing when it comes to searching bookmarks and history. It has the search-box at the bottom-right corner. Even though I know this is where the search-box is, every time I want to search my bookmarks or history I automatically look at the top-right of the viewport and expect to find it there. Then, brief moment of confusion over, I remember to look at the bottom-right of the viewport, and wonder, yet again, why the search-box is there.
Safari 9.1.2 (11601.7.7); OSX El Capitan 10.11.6.