This page is meant to be a starting point for people looking to find information why the tools don't work as expected their or why their player doesn't play a file created by mkvmerge/MKVToolNix.
mkvmerge writes new Matroska elements by default which a lot of players have problems with. See Playback does not work VLC cannot seek mkvmerge v5.9.0 for the full explanation and workarounds.
mkvmerge includes a lot of features that you can turn on and off in order to influence how the output file will be constructed. The page Improving playback compatibility with players lists them all including a description of typical symptoms.
Most articles in the playback FAQ category are also worth a look.