Star Trek

Hello, this is my first post to this forum! I'm from Finland so my English is a bit clumsy ...

I'm watching episode Star Trek Original 2x11 (The Deadly Years) and at around 5:00, in the Briefing Room, Commodore Stocker keeps saying "Sir" when he talks to Captain Kirk. Now I'm wondering why a commodore, who is supposed to be a higher ranking officer than a captain, would say so? 

I tried googling the answer but what the heck, why not come to the source of knowlegde ??? 

Nordic, my Finnish friend, movie & television writers do not always,
or even often, do their "homework," for even a broad topic. And when
it comes to the fine details, they will just make it up, or use what
they think sounds good and move on.  Like so many of us at our jobs,
writers are not looking to make extra work for themselves. However ...

I looked up Military Protocol for you. Understand I got this from the
internet. So, take it with a grain of salt. Anyway, here you go. Enjoy:

***

Someone of junior rank may address a senior officer by his or her rank
and last name, or "Sir" or "Ma'am," but they are not to use the
senior officer's first name.

Lieutenant generals, brigadier generals & major generals are all
addressed as "General." All lieutenants are addressed as "Lieutenant."
Only when writing is "First" or "Second" used.

Thank you for your reply!

I knew it could be just a writer's mistake but still I had to check if there was some other kind of a logical explanation. 

Maybe they can use the word "Sir" when speaking to lower officers just to express politeness ...

I also wondered about the title "Mr" when captain talks to some of his officers, later I found out that "Mister" means a warrant officer.