There’s a thread on the Adobe forums about this.
One person said it was an issue with Sony’s codec. But it may also be a bug in AE (depending on what kind of footage you’re using, apparently).
My suggestion would be to render out as a lossless codec (Quicktime with a PNG codec is good – NOT a PNG sequence, btw) and use something like Adobe Media Encoder to do your final encode.
Unless you’re planning to use this AE output in an editing program. In which case you should simply import the lossless file into your NLE. This would be something you should be doing anyway as encoding to a compressed format as an intermediate file isn’t a good practice.
Anyway, if your issue is the bug in AE, read the thread I linked; help is on the way.
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