MKV is a container, meaning like a zip file, that inside it contains individual tracks, like a video track, an audio track etc…
Transcoding will kick in, if trying to play a media on a player, where on or more of the trackś are not supported.
So we need to know what player you are using, as well as the media info for the MKV
support.plex.tv/hc/en-us/articles/201998867-Investigate-Media-Information-and-Formats
XML info is preferred here
/T