1. UI Issue - The Copy app doesn't support the new folder icon in Yosemite and El Capitan
2. The finder integration doesn't work, where the overlay on the finder. (Little green tick)
3. UI Issue - The Preferences View of the Copy App is suffering text misalign issue, El Capitan have new API for text formatting.
Google Chrome do suffer the text alignment issue as well (now fixed in latest stable channel).
Here is the link https://chromium.googlesource.com/chromium/src/+/1bf646e7f6ccc4a6b71a00636e1c8392223c6210
I hope that help the Copy engineer, or at least give a clue what is happening.