Starfleet was explicitly told by Grand Ruler to not try to apprehend Raven because she was too powerful. Given that she ends up killing Twilight, who's to say she didn't kill anypony else while she was on the lam?
In fact, following the above, who's to say that, if a super-powerful enemy shows up and starts killing people, Starfleet won't do anything about them because they're supposedly too mighty to face?!
A weapon that captures opponents was invented in the second season. Just how many "evil" species were driven to extinction by Starfleet beforehand?
Lots. The ones listed are only a select few out of many.
If Titan was seriously weaker during his exile, why didn't the Grand Ruler just destroy his prison and him with it after getting stronger over the centuries?
Why couldn't Starfleet fly over Violet Swamp to Blacktop Mountain to find the Titan clone (Episode 2), yet when they were challenged by his minions (Episode 16), they suddenly can? This is especially egregious, as Mykan does nothing with the Violet Swamp scene other than a song (which was later removed) and boils it down to "They did some things at Violet Swamp but now here they are at Blacktop Mountain"
In Starfleet Magic, Episode 5, how did Mysterious decide that the Waterworks building was the best place to hide rather than, say, Violet Swamp? At least at Violet Swamp, he wouldn't have had to cut off the power.
In Starfleet Magic, Episode 14, how long did Starfleet have to stay at Brain's building to where, Rep-Stallion could look into the window, see Brain's invisibility spray, get an idea, go back to the other minions and then come back?
In Starfleet Magic, Episode 23, Luna's stealth veil is described as a pure black shadow. How do the Shadowbolt guards not notice a large black shadowy veil? Furthermore, how does it mask sound, to the point where Rhymey can talk and no one can hear him?
In Starfleet Magic, Episode 25, why did Brain build a rocket when interplanetary transportation already exists in a near-instant form? He couldn't have known that they would need it to escape from Discord because most of Starfleet didn't even know Discord existed and Brain had to have started building it well before Unicornicopia was invaded.
In Starfleet Magic, Episode 26, how can Starfleet fuse 2 dead planets, along with their native wildlife and vegetation, back into existence with belief, but cannot bring Twilight Sparkle back from the dead in Starfleet Magic III or erase all evil out of the universe? How does this belief power work?
In Starfleet Magic II, why does Starfleet find it necessary to not tell anyone about the Changelings and just let them assume their friends have suddenly gone crazy?
A huge piece of Fridge Logic concerning Starfleet's very name and concept. In this blog explaining the differences between the Space Ponies and Equestrians, it's revealed that Starfleet, despite being a space-faring organization, lacks any sort of interstellar travel. Why, then, are they called Starfleet?!
Probably because Mykan thought it sounded cool. Knowing him, that's pretty much the most logical explanation.
They actually do have interstellar travel in the form of a portal network (think Stargate SG-1). Why they went with the name Starfleet despite not having anything resembling one (or how they set up the portals in the first place)... that's another story.
How old is Human Grand Ruler exactly? The story states he was one of the last men to walk on the moon. Since the last moon landing was in 1971 and based on the fact cell phones are present in the first Starfleet Humans means it has to take place around the mid-2000s/early 2010s. Since there is nothing in the fic to suggest history is different in this universe it means Grand Ruler would have to be at least fifty to seventy years old!. Ordinarily, this wouldn't be that big a deal except the story also states that he and Celestia knew each other when they were kids and it implies Celestia is in at least her mid-thirties in the Equestria Girls universe...well, you got something to add to the fridge horror section.
So either Celestia (and probably Luna) aged really well, or Grandruler's adoption of the human-verse's Starfleet characters just became way squickier. (Granted, that second one is probably the result of thinking too hard, but considering the lack of details on Celestia and Grandruler's relationship...)