I would need to see an actual link in order to see whats going on, which means, viewing the code and the actual site itself so I can inspect everything live. Otherwise it would be like shooting in the dark as I wouldn’t have any way of seeing what the issue is.
You shouldn’t have to edit the arrows as they are supposed to align naturally. Sometimes the image/thumbnail isn’t centered, or doesn’t fit the slider area, which makes it appear that the arrows are off when they really aren’t. I would recommend downloading and running a plugin called Regenerate Thumbnails – http://wordpress.org/extend/plugins/regenerate-thumbnails/ …..and make sure and run this plugin anytime you upload, or change your image, or image sizes, and this plugin will automatically adjust your images/thumbnails to fit into place. This includes slider, portfolio areas, and anywhere a thumbnail is used.