Might be non-standard pin placement, very high top weight, misaligned mass bias, blemish in the coverstock, or even a ball that was repaired at the factory due to some cosmetic issue and cannot be sold as first quality.
A ball will not be sold as an x-out because of the box it is in. It is the ball itself that dictates whether it is sold as an x-out.
X-outs are usually fine as long as you have a pro shop operator that knows how to deal with them. Sometimes you have to get creative with layouts to get them set up for your game. I have had a few over the past couple of decades and never had a problem with them.