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.
Big Lipped Alligator Moment: While several examples can go here the most infamous has to be the musical number "Shy Guy". Not only does it slow the film down, not only does it have no purpose whatsoever, but it also portrays Freddie as a slacker and makes you wonder why he isn't trying to save his friends and the entire conquest and instead partying around.
Broken Base: Almost everyone who's seen this movie has a different opinion of its quality.
Captain Obvious: The narrating Frogsinger after Freddie grew normalsized: "He was no normal frog"
No really? The first minutes didnt even suggest that.
Complete Monster: Messina is Freddie's evil aunt, and a vicious shape-shifting cobra witch who kills Freddie's father and mother with her powers, and then turns Freddie to a frog in a mad attempt for power. She then gets worse as the film progresses, teaming up with El Supremo to form a Big Bad Duumvirate, trying to trap Nessie with a boulder, and casually slaughtering her minions while attempting to dominate the world. She's also Karma Houdini, to boot, as Freddie lets her escape after the climactic duel.
Designated Hero: Freddie as an adult, is far more concerned about fulfilling his mission while being a Smug Super about it. This includes keeping disabling walkie-talkies of his teammates without their consent, treating Messina as a nuisance, despite the latter murdering his parents and letting her get away to do more horrible things. That and he's a huge jerk to everyone except Nessie.
Filler: You could cut every scene focusing on Messina away from El Supremo, and it would make the movie make more sense, have a better plot, and avoid 90% of the complaints about that movie. It has the feel of something shoved in last minute.
How did he go from a normal size frog to a human-sized frog?
Where did he get a froglike sentient car? A supposed female too.
How did he do all this and go from living in medieval times to the early 1990s?
Freddie and Messina are obviously French, but for some reason, the King has a British accent, not a French one.
What happend to the kingdom afterwards?
At one point, Freddie and Scotty are trapped underwater and Freddie gives Scotty extra air through a horn...but the horn was already fully submerged, so he was really just pumping more water into Scotty's mouth.
Narm Charm: El Supremo in general. He comes out of nowhere, is a very stereotypical villain, and laughs after every sentence he makes. And yet, he's arguably one of the more enjoyable parts of the movie. Doesn't hurt that's he's voice by BRIAN BLESSED.
Shocking Swerve: The first two minutes or so of the movie (and the title, for that matter) are incredibly innocuous and do not at all hint at the madness to come. Then we learn that Freddie's father is "a magic king" and...
Singing Loch Ness Monster Moment What does Freddy do when El Supremo is lining up his submarines to invade England? He goes to Nessie's underwater dance club and dances to a musical number with her. She even gets herself worn out and then asks what help she can be after the song is over.
Freddie's sentient frog-car Nicole could count as a SLNMM Character: She's never explained, disappears halfway through the movie and is never mentioned again.
Ugly Cute: Nessie and her family are either ugly or adorable... or both.
Unfortunate Implications: A French guy gets turned into a frog. The word doubles as a racial slur towards French people.
This is lampshaded at one point when someone tries to explain to the brigadier that he's literally a frog.
Unintentionally Unsympathetic: While Messina does horrible things to Freddie, as an adult, not only does he show the former any respect, let alone fully justified anger for killing his parents, but he's also a complete jerk to his team, not telling them information about the mission and treating them as annoyance.
What Do You Mean, It Wasn't Made on Drugs?: Messina turning into a snake, hyena, etc; Freddie now a frog growing taller, becoming a spy and getting a living frog car; singing Loch Ness Monsters, shrinking building rays; KKK and Nazis, as well as other weirdness.