In most cases, it works. Some specific files might contain video, audio, or subtitle tracks that have special encoding. If you encounter this problem, feel free to send the file to us, so we can analyze it.
Some video contains a 5.1 audio channel which is not supported by FCPX and QuickTime Player. Please select "Edit" and choose "Stereo" in the "Audio Mode" dropdown list before converting it. You can also use our OmniPlayer app which supports 5.1 audio channels to play converted files.