At the end of the App ProRes White Paper released earlier this morn there's an explicit warning about using ffmpeg:
In some instances, unauthorized codec implementations have been used in third-party software and hardware products. Using any unauthorized implementation (like the FFmpeg and derivative implementations) may lead to decoding errors, performance degradation, incompatibility, and instability.
This means Perian and other software that might use ffmpeg in some form. Clearly it's not working with the current OS and causing problems with AV Foundation, which QuickTime and FCP rely on.
I have studied this last year. Yes there are some decoding bugs sometimes. I have seen them in After Effects in some special case that you can avoid, and in some Blackmagic hardware. No issue in in most softwares (Quicktime, FCP, Adobe softwares, DaVinci etc.). Note : we are not sure the bugs comes from ffmpeg. We fixed a bug last year in the alpha encoding of ProRes 4444, since then we didn't find anything wrong besides that you should use -q 1 (Quality 1, with 4 you can have a little blur in subtle background patterns).
TL;DR : everything is fine but don't use it for broadcast.
