In Xcode 5 the position of views on the canvas does not update when constraints are applied. Thus, it is possible to have constraints that specify a different position for the view than you see it in Interface Builder. You can correct this by pressing Command + Option + = or selecting “Update Frames” in the |-•-| menu (I think it looks like a tie fighter).
Update for Xcode 8:
The “Update Frames” command now has its own button. It’s located just to the left of the Stack View / Alignment / Constraints buttons and looks like a reload arrow surrounded by corner brackets:
