The Internet claims that: "Gene Roddenberry publicly expressed his own dissatisfaction (with TFF) by stating that certain plot elements were 'apocryphal,' although it is not known exactly which elements he was referring to."
My guesses for that might include, but not be limited or even relating to:
1. Sybok - Possibly for his ability to use empathic telepathy mind control, it would surely take more than reminding a person of how they were made sad and/or abused in life to get them to become a mindless slave? Never mind how he could probe minds ever so magically
2. Scotty - "I know this ship like the back of my hand" (promptly gets knocked down by the corridor pipe shroud because he's not looking where he's going and it's apparently a funny scene)
3. Chekov and Sulu - "I believe we are lost" (because the ship's navigator and helmsman are just total doofuses all of a sudden, and it's apparently a funny scene. "The Way to Eden" had both of them given far better scenes.)
4. Uhura - dancin' nekkid (because she couldn't figure out a better way to cause a distraction than to play into sexist stereotypes and it's apparently a funny scene)
5. The Romulan seemed more Vulcan, if not a generic stick figure with much make-up and perfume you could smell from across the screen, but with no sense of cagey deceit they are known for in TOS (and TNG), looked more like a store mannequin, and had no real point to the story
6. "Go climb a rock" (what Kirk was wearing under his blue coat while climbing a mountain before he switched to his command tunic, and it's apparently a funny scene)
7. Even the electronic log book boings a spring and fails (seriously??) (because the ship made it and the ship isn't properly built and it's apparently a funny scene)
8. implied fart joke (it's apparently a funny scene)
9. McCoy - wants to sing "Row Row Row Your Boat" (it's apparently a funny scene, though he's also arguably better than, say others' attempts to sign - like
Bilbo Baggins (the video bit from "Malibu U" also has a very young Erin Gray (Buck Rogers '79) in it) and then there's that other video about a song whose title letters happen to be "L.S.D." because Shatner's covering Beatles mid/late-60s inane fully stuff...)
10. Spock = "Hold your horse" and other conscious attempts at horsing around with the script seem illogical when coming from Spock... (it's apparently a funny scene)
11. Kirk - "Plan B., B as in 'Barricade'." It's a borderline comparison to "Batman 1966" with the Riddler making riddles for Batman to instantly figure out perfectly the first time while not even needing to think for half a millisecond to come to the precise conclusion that Kirk was thinking. At least it makes Scotty a perfect Mary Sue/Gary Stu/whatever since he's doing everything the writer wants on cue. (it's apparently a funny scene)
12. Only 78 decks? Should have made it 99 decks, at which point you can have both a drinking game
and start to sing "__ bottles of beer on the wall" to make the dreadful gravity boots escape/recapture scenes pass even more quickly. And, why not, since the movie's loaded with out of place humor, they could have had Barbara Feldon do a cameo as a guard or something... (it's apparently a funny scene)
13. The crew know Morse Code. Surely at some time before saying the spelled out phrase twice would they realize "Oh, stand back. Something's about to go boom boom!" (it's apparently a funny scene)
14. Talbot smokes cigars, but then again there are numerous examples of "no smoking" signs inside NCC-1701 (bridge, transporter room) - unless those signs are 4th wall breaking regarding how every time there's a dogfight in space the bridge and/or transporter room causes a lot of smoke, and that's apparently funny?) It's not a funny scene because the Enterprise no longer has the signs and nobody's on the ship while puffin' away, so...
I'll somehow attempt to defend Klaa being an outlaw of his own people trying to find glory by destroying the Enterprise with Kirk in it and then becoming pally in the end once he gets to know Kirk for 2 seconds... mostly because "The Day of the Dove" did the same thing better, hefty shoulder slaps and all...
Actually TFF genuinely does have a number of rather good scenes, but they really had to go down the comedy road (which is probably what Shatner had been told to do by the studio, given the success of TVH. Even the lack of ILM wouldn't have felt noticed as much if the movie didn't ham it up with the humor.)