edit: It appears the reply buttons do squish like that on narrower screens though, but it's at around 1000px wide or less, so that's really a non-point in this day and age. Gradient issue isn't there though.
It is possible that some of those buttons are from add-ins like CRM, which haven't updated to the new look and feel. Visual Studio 2012 has the same problem.
Although this by no means affects your main point about the organisation/visual hierarchy.
Even obvious details are wrong like one set of reply buttons being flat and another set with gradients. This is really sloppy.