Some of the imperfections I notice are:
* The options dialog has a lot of things that just look "different". The controls are native, but the way they're positioned, etc, clearly isn't. The Mac has a lot of common things, like which order the Yes/No/Cancel buttons would appear in a dialog box, that aren't done the same in AfterShot.
* Being a photo management/editing application, it naturally uses a dark theme that looks out of place everywhere. Adobe Lightroom and Apple's now-discontinued Aperture both do this. It seems to be a normal thing with this type of application.
* On Linux, the window decorations come from AfterShot, not from the window manager. It also has the Windows close/minimize/maximize buttons.
* On an old-enough Mac, the integrated GPU doesn't provide the OpenCL stuff that AfterShot requires. This causes it to crash at startup, whereas a real Mac application would tell the OS to fire up the discrete GPU.
* I seriously doubt that it exposes any of its API to AppleScript/COM/DBUS, but I haven't checked. I know that it doesn't register itself as a source for the system-wide photo browser on the Mac (as an example, Insert > Pictures > Photo Browser in Microsoft Word on the Mac will show your Aperture, Photos, and iPhoto libraries as whatever structure they have in that application, not just as files on disk).