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Some FFmpeg encoders don't flag keyframes. The HuffYUV encoder is the most notable case of this. Every frame is a keyframe so why can't it be marked as such?
The H264 decoder doesn't set pts when decoding video stored in the avi container.
VC-1 decoder output isn't bitexact after seeking.
Somewhat corrupt MPEG2 files such as the one in Decoding artifacts,.. #31 don't produce bitexact output with repeated linear decoding. This probably indicates harmless uninitialized memory somewhere.
The best_effort_timestamp field is probably very broken in its guessing