Mocha uses QuickTime to read many clip formats. As a general rule, if you can play the clip in QuickTime it should play in mocha.
Some files however do not read correctly in mocha due to the way they have been written by other hardware or software. We have been addressing this issue in recent versions of the software.
To fix this you will need to convert the file to another format, such as a QuickTime file in the ProRes, Photo-JPG or Animation codec.
Alternatively use an image sequence, which will guarantee it to work with your system. We recommend using DPX or TIF files, but a JPG sequence is fine for straight tracking and roto.
The Mocha Pro plugin reads from your host timeline instead of the source footage and eliminates this problem.