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.
Angst? What Angst?: Freddie seems unrealistically relaxed while dealing with Messina in the climax. Considering she killed both of his parents, you'd think he'd be angrier, passionate at least.
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.
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?
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.
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.