I think that the worst thing about the Star Trek shows is that the writers often act like hack writers in an episodic TV show, with no memory from one show to the next and no commitment to realism, rather than creators of a coherent, consistent universe (compare Babylon 5, or the new Battlestar Galactica). There are many other inconsistencies between episodes.

For example, they cannot decide whether the time stream is mutable (which happens in most cases), or a closed circle (which they did in the two-parter where Data's head is found buried in 19th century San Francisco).

They aren't consistent about their own measurement system; in Voyager, it is reavealed that Warp 10 is infinite speed, which is incosistent with the description of warp speed in the original series, and is violated by several episodes in the original series where the Enterprise hits warp 11 (and also the series finale of TNG, where future ships are capable of warp 13).

There ought to be an industry rule that requires writers for science fiction shows to have passed at least high school science courses. Physics (If you're in orbit, you will NOT crash if your engines go out). Biology (Having alien DNA added to your own will NOT make you grow claws overnight). Computer science (Unless everyone is running Windows, bringing a virus-infected PDA onboard will NOT infect every computer on the ship; you can't interface your computer with every million-year-old device built by long-lost civilizations in half an hour). Common sense (The most powerful weapon system ever devised by man or alien is the TRANSPORTER. Why has no body ever realized this? There are only vague hints of this, such as when Scotty beams the Tribbles into the Klingon engine room. How about beaming a grenade onto the enemy's bridge? The possibilities are endless.)

Granted, many B Sci Fi movies make these (and worse) mistakes, but I expect better from long-lasting and respecting series like Star Trek.