If you encounter an issue where AutoTag fails to write the metadata tags to the file, I can't really do anything to fix this.
It is likely an issue with the tagging library that AutoTag uses (taglib-sharp). Unfortunately it doesn't seem to be very actively maintained so has several issues like this, but there are no real alternatives available.
The easiest way to workaround this issue is to remux the file using ffmpeg:
ffmpeg -i input.mkv -c copy out.mkv
This should not result in any quality loss, it only rewrites the container and doesn't re-encode the streams.
If you encounter an issue where AutoTag fails to write the metadata tags to the file, I can't really do anything to fix this.
It is likely an issue with the tagging library that AutoTag uses (taglib-sharp). Unfortunately it doesn't seem to be very actively maintained so has several issues like this, but there are no real alternatives available.
The easiest way to workaround this issue is to remux the file using ffmpeg:
This should not result in any quality loss, it only rewrites the container and doesn't re-encode the streams.