NGFB will ask WordPress and NextGEN Gallery to give it an image of a certain size (500x500 in your case), but if the *original* image in the WordPress Media Library (or NextGEN Gallery) is smaller than that, the WordPress and NextGEN Gallery will provide the largest image size they can, but they won't *upscale* an image. Your original image in the WordPress Media Library and/or NextGEN Gallery must be larger than 500x500.
I don't know why you would upload small images to your Media Library... WordPress works with various image sizes, all scaled down from a larger original. Your theme should be setting, and using, an image size name like 'post-thumbnail' or something else. Have a look at the "Simple Image Sizes" plugin to see and change the various sizes used by your theme and others (go to Settings -> Media after installing it).
I never thought WP and NextGEN Gallery might return images that are too small -- I only discriminate for small images in the content. This may be something I might have to add in v6.2.3...
There's no way to tell NGFB to ignore featured images -- they're featured for a reason. ;-) The only alternative I can think of might be to define a specific image for each Post and Page in the Pro version... Even then, you'd have to enter the URL to a larger image instead of specifying an Image ID from your Media Library, since those seem to be too small...
I would suggest you reconsider how you manage your images... It would be better to upload larger images, that can then be resized for whatever need your theme and other plugins have.