Actually both caps will work on both bottles, it's the difference in the bottles. The bottle on the left has a lower lip for the capper to grab on to as it crimps so you get a more complete crimp. The bottle on the right has a higher lip for the capper to grab so it does not have a full range to crimp but IME I have never had a problem with a bottle leaking.
I have bottles that are mixed like this as well and while the left style crimps better the right ones work well regardless of the caps I use. I do use the silver oxygen barrier caps on all my bottles. I have been told that if you purchase or use a bench capper instead of a wing capper the problem goes away as the bench capper does not utilize the lip for capping purposes