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@thewirelessblade There are four ways I can think of off the top of my head to do this.

1. Just getting to know the character. Every believable human has flaws. As you get to know them you get a feeling of what they are like. You explore the different directions of their personality, how they talk, what attitude they have towards the events of the world. It will probably start as a nugget. For me I get snippets of dialogue I think really fits their character, even if I don’t know exactly what their character is yet, and from there I work outward.

2. Make their strengths their weakness. Everything taken too far is a weakness. Tenacity can become stubbornness. Easy-goingness becomes having no backbone. A strong sense of justice can lead to an overly rigid worldview with no sense of nuance. The fast talker struggles to tell the truth even about small things because it is easier to lie.

3. Know what your theme is. This one only works if you know what the theme of your story is. This one is pretty self-explanatory. If you know that you are going to be exploring mercy vs justice, you give your protagonist a problem with fairness or something.

4. The Tragic Backstory card. Or just the backstory card. The way they grew up influenced them. The one who lived in a cutthroat world trusts no one. The princess could be an elitist. Even someone with a perfectly normal, healthy childhood could end up with flaws like naivety, an over-simplified view of the world, a hard time understand those who didn’t have the support growing up that they did, or struggle with feeling like the normal one in a band of epic heroes.

If by main problem you mean “My character has so many flaws! How will I just pick one to work on?” then you look at other characters and the surrounding world and ask how they would compliment/combat the weakness.