I am afraid that it wasn't just something you sensed, it was the stark reality. These people didn't know shit about evolution or science in general. One would think that with Stephen Hawking in person visiting the sets they would have taken advantage of it to pick his brain on a few things but no way in hell that they would do that. It would have impeded their ability to make up crap.
That's a bit harsh...most of the science was pretty good, especially in context of the day...the evolution thing is more of a semantics thing, they often used it as a synonym for mutation, and then folded the whole thing into exaggerated terms (much as Trek did from the sixties through) for the sake of the story...and as a way of explaining the god things and glowey life forms that Trek had picked up as part of its genesis in the sixties. Q is a God thing, like Trelane, like the Organians, like VGer....but then he drops lots of hints about evolution and humanity in particular, and suddenly there's an explanation for all the God things. But then sometimes the science Trek is about is the soft sciences, Anthropology, Sociology, Psychology...and when you compress those down for television, before you even get to the argument of whether or not you can call them actual sciences, you get the inconsistency.
Personally I have no problem with accepting that what the federation characters call evolution isn't quite the same thing we do...that's another soft science. Etymology. To them, in a universe where planet a can reproduce with planet b, millions of light years apart, things like Darwin are no longer the frame of reference. When exotic energy can mutate one being radically, instantly, into almost a different life form entirely, without outright killing them...then the frames of reference change again.
Is it unrealistic from a certain point of view? Yeah. Totally. But then so was flight, so were antibiotics, mind controlled tech etc etc. Is it totally unfeasible? Not in the frames of reference, not with the steps the story more often than not actually shows us have taken place from whichever now the story was made in and the then that Trek made off the back of it.
It comes down to consistency and continuity again I guess.
When an ancient race seeded life through the galaxy, when the afore mentioned exotic particles are there.....the frame of reference changes. And science changes fast. Dinosaurs have feathers and Pluto isn't a planet. Light is a wave, light is particle...when our paradigms shift so does our science fiction, but it doesn't invalidate it totally, it has to be taken as part of the whole. If Star Trek had started in 1866 , it would be totally acceptable for them to travel on steamships powered by aether stores, even if that series had just announced a new series for its centenary.