Finding FFmpeg issues before they happen

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Oh boy...searching for issues is impossible unless you manually examine and/or encode every single file before adding. Looking at ffmpeg warnings/issues, some are just reporting why data might be inaccurate -- the media may still function properly. Lots of timestamp issues for audio, Dolby audio-specific DTS problems, improper bits or images at the beginning of a file are inconsequential. Other times, they're catastrophic. I'm not sure being proactive about this will do anything other than cause you to pull out your hair.

You could possibly script something to check your log files and pull out warnings or errors and notify you, but hunting down the actual problem is an art form and fixing them is trial and error at best. Much of the time you'll cause more damage to the media than fixing anything.