Our animation software takes a set shape for it's mapping for logos. The shape and its placement are already set. For Live Action templates our props (like cups) have mapping nodes on them, pre stuck or drawn when we're on set. So when animators get their hands on the footage, the space the logo takes up is already pre-decided. For all other templates, the square is added as we create the animation. This square then takes your logo and puts it inside, and the max height or width fills the box. If your logo is longer than it is tall, the logo's width fills the 'input box' that we pre drew.
This is hard to fix later because the spaces are pre-chosen and decided based on key aesthetics and what overall suits as many logos and images as possible. I have a video from our Head of Animation who explains this with his visual guides, should you wish to see this: Here
In short, one way to resolve this is to use an editor to zoom into the entire animation clip. This will not make your logo any bigger but simply make the clip zoomed-in entirely. A final option would be to consider a 'favicon' version of your logo. Something more square or circular, which lots of brands have in their brand books, for use on icons, tabs, social media accounts and letterheads.