[Help] Colours change after exporting animation.

Sadly, Zeranoe has stopped building ffmpeg but alternatives are now linked to from the main ffmpeg site:

I have a feeling that you’ve taken a screenshot of a paused video player while it was playing the .mp4 output file. Is this the case?
If so, you’re at the mercy of the video player that you’re using.
Krita (and ffmpeg) can not be responsible for the performance and fidelity of any video player that is used to play the output .mp4 file.

You could try a different video player. VLC is very good and well regarded and is free.