Not a Mac user, so I'm seeing this for the first time. At first I didn't get what you meant, but the longer I looked the more things I found that bothered me.

Here's a list (feel free to add things):

• corner radius on rounded edges is too large
• sidebar menu blends poorly with the rest of the UI (lighter color, white frame, no horizontal padding)
• status line at the bottom is inefficient (could be one line instead of two, not sure why one has a close button) and seems inconsistent with the rest of the UI (thinner lines, no padding at the line ends)
• horizontal separators in the file tree are too thick (makes them look like scroll bars)
• tabs at the top look like a giant toggle button (not like tabs)
• buttons on the top right have a white background that seems unnecessary (the active button goes from light gray to white to medium gray, which is too busy)
• forward/back buttons on the top right have inconsistent design and look like one of them is active
• colors for active elements in the outer UI don't match (light gray in the sidebar menu, medium gray for the top buttons, white for the tabs)

This is just visuals. I can't judge the functional aspects of the design.