Recall in The Original Series:
-The galaxy seems to be about the size of North Dakota, and has a mysterious force field around it that prevents ships from leaving - the ENTIRE GALAXY. The galaxy is divided into four quadrants, whatever that means. We seem to have covered over a trillion star system in less than two hundred years, and have a bureaucracy and navy large enough to cover it all.
-Most aliens are essentially college educated humans, sometimes British, that somehow we can have a common basis of understanding with.
-All time is the same time. Relativity and frames of reference don't exist.
-We can mate with aliens. Either because of parallel evolution (up to the point where a Roman civilization exists that matches and expands on our own, and a Starfleet officer can manufacture a Chicago Mob planet from a book), or because a alien Apollo seeded us, or there was a central human-like race that spread across the galaxy, becoming all those English-lit degree holding cultures. Take a pick.
-Planets only have one climate.
-We can speak all languages, because of a translator. How does that work?
-Disintegrating a person, turning them into photons or whatever, and rebuilding a copy far away doesn't kill that person. Lampshaded when the transporter buffer created two Kirks. It could have made a million Kirks. It always can. The real one died the first time they flashed him.
-The Enterprise requires engine power to maintain orbit. This was a plot point. That's not how orbits work. Generally you stay up.
-Absolutely EVERYONE starfaring in the galaxy is at or just about our level of technology.
-Biologically divergent microlife doesn't eat us immediately.
-We somehow can't figure out the ageing process in 300+ years, and how to counter it. We can't even cure baldness.
-What happened to Kirk's avowal of the Christian religion in the Roman culture planet? "The Son, not the Sun". Seems to have gotten in there somehow. Awkward.
-We have inertial dampers that kill millions of gees of acceleration, yet they still fly around like dice when someone taps on the hull. No safety belts? No secondary vernier fine-tuning dampers at least on the bridge?
-No money, yet there is trade using money.
-What exactly are they mining out there that they can't synthesize? They keep implying they need certain rare minerals. They have 3d printers that can make anything from raw elements! What magic is dilithium crystals made from? Latinum? Why are there MINERS?
-Why in the Force are they messing about with planets, with actual life on them, for colonization when they can make artificial habitats with billions of times the surface area of any planet from raw materials floating around and between the stars? Elon Musk has the same blindness about Mars, mostly 'cause he thinks Star Trek is SF. Planets are not the answer, especially since our colonists will murder anything in their way, one way or another. It's a pre-1970s SF blindness.
-Why do all ships fly so damned close together, emulating the Pacific Fleet around 1943? Why are they all oriented in the same direction?
-There were 12 -TWELVE- Constitution class ships in the entire galaxy. A trillion stars, a 3D object a hundred thousand light years across. Yet we rule the waves?
They've time travel on demand. They don't have a time exploration corps? Really??? Holy Connie Willis, have they no need to travel to the Blitz?
Who is in charge, Starfleet? What is their government?
Where is all the wo(man) power coming from in only three hundred years? Even at full bore baby firing, we can't spread out that fast. Not enough people.
Lots of things were silly in TOS.