Don't think specifically in terms of 'giving' a character 'flaws' like you're picking a list from a D&D handbook. You're not stapling a negative character trait onto an otherwise complete character. The positive and negative character trains a character has are defined by circumstance and wholly integrated into who they are.
Think in terms of what your character wants. Goals are a much easier starting point for constructing a character in my experience. The things they want will define what they focus on, what they train or practice vs. what they ignore or neglect in their life, and that will make it much easier to build your character into someone that feels fully fleshed out and developed.
There are absolutely no personality traits that are inherently positive or negative. This is writing advice, but it's also just my general philosophy and overall life advice.
Someone who is domineering and aggressive can be a rude asshole when there's nothing super important or urgent going on, or they can be a confident leader who gets shit done when the chips are down and there's no time to waste, it just depends on circumstance.
Someone who is fearful and quick to run away from a conflict can be a pathetic coward if they leave an innocent person to die when their intervention could have changed the outcome, or they could be a quick-witted survivor who didn't throw their life away for no reason when they're the only one to get out of a dangerous situation that was clearly too much to handle.
Any sort of 'negative' personality trait or 'flaw' a person can have is also capable of being a virtue or a positive trait in other circumstances, and vice versa.
Ned stark is honorable, honest, and determined to do the right thing when he's the ruler of Winterfell, but that same honor and honesty cause him to almost throw the kingdom straight into another civil war when he gets into King's Landing.
Jesse Pinkman is a defiant, lazy, ill-tempered punk when he's stuck in standard middle-america trying to fit in to highschool, but those same personality traits make him the perfect defiant rebel willing to stand up for what's really important when he sees just how far gone his former mentor has become.
Thinking in terms of straight-up 'flaws' a character has runs a risk of making you think of your characters as perfect except for this one trait you duct-taped onto them. Those flaws can often feel incongruous because they weren't organically developed as a natural result of their goals, principles, morals, and circumstances and were just added for the sake of your character not actually being a Mary Sue.
Not saying that you're doing that, necessarily. I haven't read your story nor do I know your character, so obviously I'm not accusing you of anything. It's just a trap you can easily fall into if you're 'adding' flaws to a character, instead of building a character that has flaws due to the natural way their personality traits, desires, and environment will develop them.