For instance, black bars at the top and bottom of a video clip will be included in the rendering process.
This also happens, e.g. if you are using HD material in SD projects, and the video editing program passes video data to the Mercalli plugin that are not based on the original HD footage but on the downscaled version. Such a clip will also have black bars at the top and bottom.
An easy solution: simply slide the “Important image area” control (for assessing camera shake) from the “neutral” setting towards “centre”. The border areas will then be ignored and stabilisation will focus on the actual important image areas, which, however, will also be reduced on the left and right.