It at first seems baffling that Sousuke's teachers wouldn't suspect his guns were real, until you realize that Japan has very strict weapon control laws. Seeing even just a handgun in real life is unthinkable for a Japanese civilian, to say nothing of the military-grade assault rifles that Sousuke was packing.
Sousuke's inability to realize the fuss about the Sacred First Kiss might appear strange until one realize that he grew up in Afghanistan, where kissing (between men) is simply a form of greeting with no romantic implications whatsoever. In episode 8, he even revealed that he had kissed men before during his time in the Middle East and Central Asia.
Why is Kaname an extra harsh tsundere? And Tessa so openly flirty for her age? Their heads are always filled with whispers, so to get out what they think for themselves they say it out loud.
Related to that with Kaname, the whispereds get the thoughts of geniuses from the future and the past almost all the time, her having conservative opinions about how men should act probably comes from hearing the voices of old.
That idea is sorta confirmed by Satsuki Yukino herself. She mentions in an interview for the "Full Metal Panic! The Anime Mission" guidebook that the production crew told her to act as if Kaname's a middle-aged man.
The idea for the Tactical Division to send in a SRT/PRT unit made up of operators who can easily pass themselves off as East Asian based on their physical appearance make sense once you realize that the briefing was meant for them to infiltrate the divided Hong Kong region. They can pose as locals (or East Asian expats) with working jobs in the region.
One for the OVA. Another reason for Clouseau's rage at Kurz tampering with taping over his DVDs with images of pigs kissing is because of the grave offense to his religious sensibilities as a (implied) practicing Muslim who would consider pigs Haraam and understandably would be livid at seeing them gratuitously kiss in an overblown pornographic fashion.
When you rewatch/reread the novels on why Clouseau was getting a rise out of Sousuke at Merida, you can see that at one point in his life... Closeau acted like him at his age and wanted to see that Sousuke does not make the same mistakes during a field op. It's basically his perspective of I Hate Past Me.