Hi. I am sorry both you and Rocky is going through this stressful period, and that two lots of surgery have been required, hopefully which will resolve the problem and return him to feeling better and healthy again. Stones can be missed, either because they are small and not obstructing anything - or because of an error (vets are human and occasionally they do miss something). Stones tend to be more serious in male dogs, because they can block the urine passage, which is a situation far less common in females. The other problem is that some dogs are 'stone producers', and this means even when the surgery is completed, you will need to 'manage' his condition for life. This will certainly involve a new kidney-stone specific diet - which your vet should fully explain to you, but if they don't, you MUST ask about it.
Let us know how Rocky goes with the surgery. Fingers crossed it all goes well.