: How do you know when there's something missing in your story? You always hear about what has to be removed. Usually unnecessary stuff that doens't contribute to the plot. How about the opposite?

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There are two approaches. What SF already pointed out is the most easy, the unstructured one. In any case, for many reasons, you should give your story to someone to read and give you quality feedback. I've also had good experience reading it (aloud) to someone and immediately writing down whatever they say or ask. But that requires special people and circumstances.

The structured approach works if you start your work like that. Do you have an inventory of all your locations, characters and storylines? If so, you can check them for completeness. If you maintain these meta-data well, they will provide not just the outline, but a good review of them also will tell you any holes. For this, make a short checklist of what matters to you. Do you need closure for characters (as was mentioned already), do all your characters and locations have to be linked to each other? Do you want a physical appearance description for every character (sometimes you want to leave it up to the imagination), etc.

Basically: To know if something is missing, you first need to know what should be there.

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What is in your head and what is on the page may be very different things. The characters, places and developments of your story may seem a tightly woven tapestry in your head. But the fresh eyes of another will clearly see loose threads, tears and great big holes in the fabric. Always be open to the critiques of others.

That being said...

By all means, do trust your "gut". Perhaps you do know better than anyone what (for example) your protagonist should or shouldn't do. If you want to follow that feeling, then attempt to be as specific as possible about what it is that feels wrong. Can you explain how, objectively, that part that bothers you does not integrate with the rest? The finer the level of detail you can muster, the more certain you will become.

The two previous are examples when the holes are subtle. In contrast, when I'm writing, the most blatant signs of lacking content I run up against are things like:

An unintentional unevenness in the pace. Does an incidental travel scene take up more pages than events leading up to the conversation that informs the moral dilemma of the of story? Perhaps trim some descriptions of the quality of light on the trees, and unfold more of the character's inner frustration at their own inability to articulate their beliefs.
Actions that advance the plot and are consistent with the character and the world (as known to the writer) but have no previous mention in the text itself. During a sweep of revision it can be worth combing back through the text to check that all elements that combine in the central events of the plot have some seeds planted previously.

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Best get someone to read it. Some seasoned writer is good, but anyone will do, except close friends and family who'd praise you no matter what abomination you produced.

You too, let your story sit for a couple months until you forget its key points and try to read it "as new". Still, it will never be quite as efficient at catching simple omissions: missing tags in confusing dialogue, too skeletal location descriptions, thought shortcuts, your assumptions about reader's knowledge, etc.

OTOH, there is a significant piece you can spot for yourself without external help: closures. List all characters; more or less significant. (include significant non-person actors too). Recall all more significant actions they performed. Think of their consequences, a week, a month past the ending of the story. Do they get away with their shenanigans? Do they receive honors? Do they recover? Did they learn something new?
Cull the ones that really, really don't matter, and check whether you included all the rest. Make sure every thread, every event received a closure.

Speaking from experience, as a reader - I often focus my attention at some background characters and really just keep reading to receive the closure on their specific thread. Say, two minor flunkies of the villain who happened to be exceptionally nasty jerks, and appeared early on, bullying the protagonist. Then I witness the rest of the story: the struggle, the growth, the challenge, the battle, the epilogue - but the two presented early on never appear again, their fate is never even implied. And I don't care about the ending. I didn't receive my closure and I'm disappointed!

So: Close all your threads, and you don't need external help with it.

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