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.
Information by version number
Current versions: the GUI/mkvmerge crashes when starting to mux
This happens with recent AMD processors due to bugs in said recent AMD processors. BIOS/Firmware upgrades should fix the problem. See issue 2589 for details.
Current versions: Error message "JSON output could not be parsed"
It seems that certain anti virus tools prevent mkvmerge from getting executed properly. See this FAQ entry for more information.
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.