Hello 
I checked the site and it seems there is no custom css or other customization which affect the thumbnails.
This should be a site setting misconfiguration like:
But you said:
By the way what is the default value on your min ratio to crop setting?
Maybe a CDN misconfiguration? If you use a cloud based image resizer to optimized images (thumbnails). This is not very likely but this could be also a possible reason.
An other possible reason is a plugin which can do things with thumbnails. As Simon suggested you can also try upload new images in safe mode to check this might caused by a plugin. (but as I saw, you don’t use such a plugin.) If I am wrong and you use any plugin like this, sometimes disables the plugin on admin is not enough, in this case you have to comment out (remove) from app.yml and try again…
But note that: These thumbnails are cooked in these sizes and cropped in posts. So if you change anything it won’t affect the existing thumbnails until you rebake the posts or resize these manually to recognize it the system as new file and generate new thumbnail for them. With new uploads these changes should show the changed result after reload the page.