I see. My guess is that the logos were uploaded before version 8.1 (which was only released about 4 months ago). Unfortunately, the logo scaling and cropping was applied to the logo that was uploaded overwriting the version that was uploaded. This pretty much exactly how WordPress works too except Connections added a margin as needed to make sure the image was at the size set on the settings page. So, previous 8.1, the only way to change the scale and crop of a logo (images too) was to reupload the logo/image. With that said… the only way to get rid of those margins in this case is to reupload the logos.
Version 8.1 and greater has far superior image processing now, the image/logo settings can be changed at anytime and Connections will create new the images as needed, never affecting the original (one exception) uploaded image/logo. (WordPress does not even do this natively at present, you need a plugin.)