We can crop images. Can we crop videos?
it's not as simple as images
but it could be as easy as the correct specification of the video but there is not enough information.
in the decoding settings, you can manipulate video pixels by geometry, ie, anamorphic, squeezed, stretched and also player/browser settings, the image window or player window, you can specify a small player window and a magnification level. if you allow or disallow zoom/magnification, you'll force an offscreeen draw or black bars.
i would encode to the correct size and platform for best quality, these kinds of fixes are 'kludges' but they work in a pinch. i would grab the quicktime sdk and poke around.