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.
Asspull: Q never once explains to Bond that the infra-red underwater camera has a built-in Geiger counter (only that the watch does) which comes as something of a surprise when Domino uses it later on in the film. (In the commentary, actor Desmond Llewllyn complained that his favorite part of the Q scene ended up on the cutting-room floor; perhaps the explanation was part of that bit.)
The film was set to go with Warwick's version of the theme, but at the last minute the producers insisted that, no, the theme had to have the word "Thunderball" in it, so a new song was hastily written to be recorded by Tom Jones and parts of the film were rescored to feature the instrumental version of that song as a leitmotif. An instrumental version of "Mr. Kiss Kiss Bang Bang" is heard at various points during the movie as a kind of secondary leitmotif. The producers planned to use the Warwick version of "Mr. Kiss Kiss Bang Bang" over the end credits, until Shirley Bassey sued.
The Dionne Warwick "Mr. Kiss Kiss Bang Bang" is featured in its entirety on the secondary commentary track of the Thunderball laserdisc/DVD/Blu-ray.
Bond clobbering the SPECTRE agent in the opening is basically a well staged and hard hitting fight scene but it's undermined by the fact that the SPECTRE agent is in DRAG.
Bond on the overcranked stretching machine Death Trap is supposed to be something that has the audience on the edge of their seats, but it just looks ridiculous. Quite frankly, he looks like he's humping the table.
The name "Disco Volante". Yes, it means "Flying Saucer" in Italian, but "disco" has other connotations nowadays.
One-Scene Wonder: Patricia Fearing the nurse, especially when she's being massaged.
This is true on a larger level, too. Due to a dispute with her agent, Fearing's actress Molly Peters was unable to follow up on the career bump even one-scene Bond girls usually got—she never landed another major film role.
Seinfeld Is Unfunny: The plot using a nuclear weapon to extort a ransom was considered a unique idea when this film came out, now it's arguably the most cliched Evil Plan in the book.
Shameful Strip: Bond arguably does this to Patricia the nurse— in a public sauna of all places— when he blackmails her into having sex with him. The "no means yes" style smile does not make it easier to watch.
What an Idiot: It's probably not terribly wise to go around wearing the logo of an international terrorist organization on an oversized ring if you don't want to tip off the secret agent you just picked up that you're working for the enemy.
Woobie: Domino, she's the mistress of a sadist, her brother gets murdered and Bond is using her to get to Largo.