Here is a non-exhaustive list of links to threads containing information about known FS-UAE problems. With problems I here mean "FS-UAE not working as intented", people may consider some features problematic, but that's not what I mean here ;-)
Likely to be common issues:
Portable proxy launchers Launcher.app and Arcade.app does not work on macOS Sierra
http://eab.abime.net/showthread.php?t=84196
https://github.com/FrodeSolheim/fs-u...cher/issues/49
Problems docking FS-UAE on macOS Sierra
http://eab.abime.net/showthread.php?t=85460
https://github.com/FrodeSolheim/fs-uae/issues/145
Rare issues:
On computers with little physical RAM, may not be able to use Zorro III memory
http://eab.abime.net/showthread.php?t=85257
Some experience mouse pointer issues with mouse integration enabled
http://eab.abime.net/showthread.php?t=84871
Not reproduced by FrodeSolheim
(Will go through forum threads and add more links to this list)