So I have no other choice but to conclude that you’re talking about an evolving animal that, for billions of generations, used two breathing systems simultaneously (extracting oxygen from both water and air).
More likely, just millions of generations.
That would be an incredible mechanism, and one that would surely require perfection in order to operate! Tell me more about how that second (the alternate) breathing system is operational while it is undergoing slow development over those many generations of offspring.
And here is where you are wrong. It most certainly does NOT require perfection or anything approaching it. All it needs is to be able to add to the oxygen acquired from the primary system.
Many animals alive today have more than one mechanism for getting oxygen onto their systems.
For example, many frogs have gills when young, lungs when older, and *always* have significant oxygen transfer across their skin. This is true also for other small amphibians (getting oxygen from transfer across skin requires both a moist skin and a small enough animal that surface to volume ratio is high).
Many fish are able to move across land, going from one pond to another while using primitive lungs (few elaborations into bronchi, for example). They will also use gills while in good water.
Many types of fish will gulp air, especially in ponds that are oxygen deprived.
The point is that a breathing system is primarily a way to get oxygen into the blood system and waste gases out. ALL that is required is a membrane exposed to oxygen and blood vessels to pick up that oxygen. Fish mostly get their oxygen from what is dissolved in the water using gills (which use large surface area to get more oxygen out), but will also get it from across skin or from lungs/swim bladders. Different fish, depending on their environment, have adapted very different mechanisms.