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
Only on Windows: The GUI (mmg.exe) has been linked a newer version of the wxWidgets GUI toolkit library than the previous release, 7.5.0. This results in two issues:
If you right-click on any input, open the »Insert Unicode character« sub-menu (even accidentally) and then close that sub-menu again then a crash message will be shown.
Deleting entries in the chapter editor will leave the chapter editor in a semi-unworking state. You will have to click on another entry before any of the controls start reacting again; however you will also receive an error message that the UID is not valid/not set.
Both issues have been fixed in new pre-builds by building against the same version that 7.5.0 has been build against.
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.