If your project settings in Mocha do not match your host, it can result in drifting or misalignment.
Quick Tip: Make sure the FPS, Project Dimensions, and PAR (pixel aspect ratio) settings are the same.
If you use After Effects there is a common issue when a source insert is not the same size as the After Effects composition: the tracking data pasted in from Mocha will be misaligned relative to the difference in the source. This video tutorial covers 2 simple ways to solve this issue that works for both Mocha AE and Mocha Pro inside Adobe After Effects.
These workflows will also work in most other host applications:
Align Surface method - Insert is already positioned before Mocha
Align your insert in your host, precompose or nest your insert depending on the host, and in Mocha, use the Align Surface tool on the same frame you synced up in your host, then apply the corner pin to the entire precomped or nested layer. This technique is also very useful for paint fixes.
Fit to Comp method - Insert is set to Full Screen
In this technique, you scale the insert layer to the size of the comp. Precompose or nest the insert, and then apply a Mocha corner pin that fits exactly to the area you want your insert to be.