After writing the beat sheet, you end up realizing you need to put a lot of filler scenes and make your characters make some small talk and say things like "How is it going?", "How are you?" and so on. Is there a guidelines on what to write and what do these filler scenes have to achieve exactly? Some of these small talks don't advance the plot, so I am thinking maybe I am doing something wrong, because I think we can remove them without changing the plot.
You remove them. A "beat" may be multiple scenes, in fact in screenplays beats may be several scenes. The second Act of Ocean's 11 is basically the two main guys recruiting the other 9, and it is a series of a lot of scenes, often 2 or 3 for a recruit, All for one big beat: Ocean assembles the rest of the team.
Peter Parker gets bitten by a radioactive spider, and turns into Spiderman. But that takes up several scenes.
Don't include any banal bullshit in your story. Everything you write is there to convey something important, even if on the surface it seems banal; it can be a shift in a relationship, for example.
Do not write scenes where nothing happens and nothing really changes, for either the characters or the audience. (It's okay if nothing changes for the characters but the audience learns something new.)
Every scene has a purpose. Break and restart later. In a screenplay, you can put a super on the screen.
JOHN What now?
Allison leans back in her chair.
ALLISON Now we wait.
SUPER: "Two Hours Later."
Allison, leaning forward in her chair, tells John a story, he's grinning, she's enjoying herself.
ALLISON So I'm completely naked, and--
The phone RINGS.
ALLISON Crap, here we go.
She picks up her phone.
You can do a similar thing in a novel. if there is time to kill, skip forward. If you want a transition, do something interesting to convey how the time was passed, but don't overdo it. A paragraph, 50 words or something. A quarter page. I never have to follow up on why Allison was completely naked in her story. Or maybe in a few chapters John wants to hear how the story ends, and she tells the whole thing.
Doesn't matter. "Filler" passages where nothing happens are the death of a story, they are boring, and getting bored by pointless reading is one of the big reasons readers lose interest and put stories down.
If your plot allows, you can break away when the boring wait starts to something else, another character, the villain, where something is about to change.
Otherwise, just skip it. Readers don't expect to see every minute of your character's lives. They don't have to go to the bathroom unless there is a plot reason to get them out of the room. They don't have to sleep, skip time and start the next morning, we will assume they did stuff and went to bed and woke up and got dressed and got out and now something interesting is about to happen. If they have to disappear for a year and come back,
SUPER: "One Year Later."
Rowling opens Chapter Two of her first book (Harry Potter and the Sorcerer's Stone) with "Nearly ten years had passed since [...]". She skipped forward ten years. No explanation, because none is needed.
Chapter One ends with Harry Potter a rescued infant. In Chapter Two Harry Potter is eagerly awaiting his 10th birthday. No need to provide all the boring mundane details that happened in-between, Harry learning to walk and talk, attending his first day of school, blah blah blah.
Don't write the boring parts.