http://www.cheatsheet.com/entertainment/things-star-trek-make-no-sense.html/?a=viewall

Robert Yaniz Jr
May 01, 2017

It’s amazing how recent years have seen geek culture explode into the mainstream. Superheroes, sci-fi, and fantasy are now all among the most popular stories permeating both film and television. But even so, few fandoms are as passionate about their franchise as those who hold Star Trek in high esteem. Last summer’s latest entry in the film series, Star Trek Beyond, was a modest success at the worldwide box office and garnered solid critical notices (despite its problems), and the upcoming Star Trek: Discovery will bring the beloved franchise back to its television roots.

However, as much as Star Trek fans hate to admit it, there are some elements about the series — and, yes, the same can be said of other franchises (looking at you, Star Wars!) — that can become frustrating over time or just plain don’t make any sense. For a multimedia franchise with 50 years of storytelling under its belt, perhaps that kind of thing is bound to happen sometimes. In any case, here are our thoughts about some parts of the series that confound us.

It would be great to beyond Starfleet.

2. All the aliens are humanoid for some reason

It was explained.

From the pilot episode of Next Generation:

After studying the ambiguous number blocks for hours, the discovery is made that these fragments are compatible DNA strands which have been recovered from different worlds all over the galaxy. The crew eventually believe that they have discovered an embedded genetic pattern that is constant throughout many different species, and it is speculated that this was left by an early race that pre-dates all other known civilizations. This would ultimately explain why so many races are humanoid.

https://en.wikipedia.org/wiki/The_Chase_(Star_Trek:_The_Next_Generation)

Of course the real reason goes back to the original series, and it was simply budget constraints, Spock almost didn't even get his pointed ears. That's the reason Klingons in the original series are just guys with beards, they did want to go into more detail with their make up, which eventually happened in the films and later series.

That was NOT from the pilot episode. But from a sixth season episode.

Ed.