(Apologies for the super nit picky bug report, but it seemed borderline worth filing, it becomes more noticeable the more neighboring comments you have to hide)
Steps to reproduce: Create an inline comment on a revision on a line that has a number >1000, hide the comment. The column where the 'Show Hidden Comments' bubble appears can't fit both the line number and the bubble without line wrapping, which also pushes what looks like an empty line into the diff.
Version info:
* commit ab4355cde0f8913b9e12be345f813f5ba7e0e468 Author: epriestley <git@epriestley.com> Date: Sat Jan 21 08:11:19 2017 (stable) Move Favorites and User menus to MenuBarExtensions
It looks like the line number column has a fixed width of 45 pixels.