These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Samir Duran has psychic powers. The only explanation for DuGalle's actions that isn't blind idiocy and incompetence is Duran altering his mind. As a Ghost, he is required to have a certain level of psychic ability (which all Ghost abilities rely on in order to be used). Considering the secret hints that he may not be entirely human, this is entirely possible.
Is Arcturus Mengsk a loyal soldier of the Confederacy who was left as bitter and angry as a man can be after his father, mother, and little sister were murdered by Confederacy Ghosts? When he "betrays" Kerrigan, he calls her an 'animal' that needed to be 'put down.' Fun fact: his father's head was never found. He's been using her as a tool against the Confederacy for years, but all the while knowing full-well that she was one of the three Ghosts who murdered his entire family. Her disloyalty to the Confederacy was a mere coincidence that stalled his execution.
Anticlimax Boss: In mission five of the sixth campaign, you're pitted against a super-powered Dragoon who can be killed instantly with the Queen's "Spawn Broodlings" ability. The second boss, a super-powered Battlecruiser, can be rendered helpless with the Defiler's "Dark Swarm," which blocks all its attacks on ground units. Then again, these are there purely to let players see how useful these abilities can be.
Complacent Gaming Syndrome: Many players only play Lost Temple, Big Game Hunters, Python and/or Destination. From the user-created side of things, we have Fastest Map Ever, which was designed initially to speed up the beginning game by stacking minerals directly next to the beginning buildings making mining for resource instantaneous. To say that there are several variations of the map would be an Understatement.
Anything at all concerning Duran. The fans have had more than decade to speculate and some very strange, exotic theories have been put forth.
Some insist that the factions are expies of the Imperium of Man, Tyranids, and Eldar, and StarCraft is based on 40k. (With 40k being based on numerous Sci-Fi works, it isn't really a surprise.) And the reverse was guessed as well, some claim the Tyranids were changed in appearance to match the Zerg better and that the Tau were based off the Protoss.
Idiot Plot: Brood War. If a couple of characters had spoken up before their deaths, Kerrigan's entire plan would have been ruined. Also, leaving the UED in complete control of a mature Overmind, and thus in complete control of the entire zerg Swarm, including Kerrigan...That would have been just awful.
Well, it's pretty heavily implied that they were gonna use the Zerg to wipe out the Protoss. Something Kerrigan would probably do on her own, though.
Lady Mondegreen: Not the names in particular, but the quotes units (Mostly Protoss) say get misinterpreted, especially the Khalai language ones.
Marines: "You want a piece of meat, boy"!
Zerg Guardians might sound like they're saying "Brood War!" once they finish mutating.
When Zerg upgrades and research are done, it says "Evolution complete!", but for some, it may sound like "Caboose incomplete!"
When Zerg hive clusters are under attack, it could be interpreted as "Die Cloyster is under attack!"
Zealot: "My life for hire!", "My wife for hire!", and "I am a fryer/friar!" (My Life for Aiur)
Probes and Reavers sound like they're saying "Protoss!" One Probe line sounds like "long ago."
One quote the Dragoon says sounds like it's saying "Stop killing us!" (Khalai language), "Galactois" (Khalai Language), and "Thank you something" (Make use of me)
Dark Templars sound like they're saying "Yeah squeal!" and "Give voy!"
Dark Archons might sound like they're saying "Must inflame us!" (Thoughts in Chaos) and "Old Navy in the way!" (Oblivion awaits)
High Templars might have sounded like they say "It's one hell of a party!" (Khassar de Templari),
And one of the Archon's select quotes may sound like it's saying "Oh shit!"
One of the "attack" quotes of the Scouts sound like it's saying "Lucas sectionized" (Locus acknowledged).
Arbiters. Yes. "We are fisherman" (We are vigilant), "Goodnight wing", "In chastity", and "Jikakazoid".
Padding: Some missions are obviously there just to fill up the quota of 10/8 missions between the base and expansion campaigns, having little plot development that couldn't have been handled in another mission much more simply. Perhaps the most blatant examples are Episode IV Mission 5 and Episode VI Mission 6. The former, your enemy is just a distraction from the actual goal of the campaign and is barring your path, the latter, you get attacked and defend yourself.
Ironically, there were two missions cut from Episode I, Biting the Bullet and Operation: Silent Scream because they were seen as this exact reason; especially the former mission. Another reason for the cut was to even out the campaign level totals so that each race was given ten levels.
Porting Disaster: Starcraft 64 is generally considered this way, which is unfortunate, because it really was pretty damn good. Being able to control 18 units at a time rather than 12 is a pretty major jump. On the down side, most of the voice acting and FMV were removed, something expected for that console. The cartridges simply didn't have the amount of space needed for all that.
Rooting for the Empire: The United Earth Directorate overthrew Mengsk and temporarily dissolved the Dominion, enslaved the Zerg and took control of them, and used their power afterwards to try and take down Kerrigan's Brood...why was everyone so opposed to these guys again? Okay, granted they come on behalf of the same government that exiled your ancestors to this sector of space, but still, they took out two of the major evil powers in the sector and probably would have taken out Kerrigan too if Raynor and Fenix hadn't helped her. If they had stopped to consider negotiating a deal with the UED, which the UED would have at least considered since DuGalle and Stukov are Reasonable Authority Figures, Raynor and Protoss should have been helping them!
Until you see their bases in one of the Zerg campaign missions and realize that they are infesting their own men.
The Scrappy: Competitively, the Protoss Scout is seen as this for costing too much minerals and gas for the little that it can accomplish; which only sees little use to take down bulky enemy air units.
Scrappy Level: Brood War's "The Insurgent" level which many will agree has some of the worst storytelling seen from the original story campaigns. Aldaris' What an Idiot moment aside, the worst of it is actually that players are supposed to believe that not a single rebel Protoss other than Aldaris knew what they were rebelling for.
Units lining up single-file when they walk long distances
Not being able to rally workers to mine minerals/gas when they spawn.
Ramps in general, especially the ones for the installation missions, which are just too shallow a choke-point to traverse.
Seinfeld Is Unfunny: While still popular, they are definitely areas where the game shows its age, like that most multiplayer matches consist of rushes or unit spams, and most of the campaign missions consist of objectives that always boil down to "destroy the enemy base", which in later missions take up most of the map.
So Cool It's Awesome: The original game is frequently called one of, if not the best RTS ever. Hype Backlash and Seinfeld Is Unfunny has come into play over the years, but the game still holds up well up unto the release of the sequel, and probably will continue to do so for some time.
They Wasted a Perfectly Good Character: Daggoth, the senior Cerebrate to the player in Episode II, gets no screen-time at all afterwards. Only that he led the formation of the second Overmind in the expansion due to the death of the original Overmind...and yet he doesn't get a single line of dialogue, and takes a Word of God stating that he died to Kerrigan sometime off-screen.