Quite frankly, if the vet doesn't know how to properly euthanize a reptile, then I'd be kinda hesitant to go to that vet....
No, sometimes the sedative isn't quite strong enough...so you give them more. This is what my reptile vet does. Reptiles are quite sensitive to sedatives; too much and they die. If the reptile just goes unconscious, then it wasn't given enough, and the vet gives it more. Once the reptile is sedated, it's not going to feel anything anymore.