This may be because of the width / height of the embed in your html. You can try tweaking that.
The simplest fix, however, is drawing a "border" around the outside of your Catalyst project that is the same color as your web page and will cover up any content outside the project. Peter wrote a longer post on this in the past, but I haven't been able to locate it.
Here are a couple of posts from Adam and Peter covering masking techniques which may help you:
Adam: You can do crude masking by placing your content into a custom component (for example, a rectangular shape); double-click the component to enter edit-in-place mode, then choose Modify > Auto Size Component Bounds (to uncheck it, because it is checked on by default), and then Modify > Clip to Component Bounds (to check it on). You will now see some crop marks that are the clipping bounds of the component. Objects that go outside these bounds will be invisible ("clipped") when the project is run.
Full discussion here: http://forums.adobe.com/message/2532197?tstart=0
A bit more elaborate technique posted by Peter, incorporating Illustrator with Catalyst: