For me, most of the conflict in my stories are created by the characters, so their characters develop, flaws and all, as I plot out the story itself.
For example, my villain in last year's NaNo was my Male Main Character #1's partner. He got killed because a summoning went wrong and MMC1 ran off at the first sign of trouble leaving my villain to die. So just by figuring out why my villain is out to get my main characters, I learned that MMC1 is untrustworthy, easily panicked, and puts self preservation above altruism. The rest of my characters develop that way too. Conflict is needed, so I often make my characters do things to get themselves into trouble (as opposed to trouble finding them regardless of their actions, which still happens but them causing their own misfortune is so much more fun), and that helps me give my characters realistic flaws that have actual consequences in the context of the story.
Now, I'll always start off with a general idea of the character's personality. I'll sit down and write out their past and how it made them who they are, so I already knew MMC1 was going to be selfish, self centered, and self pitying before I started much plotting, but that really helped round out those flaws in a realistic context.
So I guess my advice boils down to: stick your characters into situation, and make them make it worse, or cause it. Maybe even just write a couple of short stories outside of your novel to get a feel for them. If you have to make them get themselves into trouble based on their actions, you'll be forced to come up personality flaws that get them into sticky situations. Also, they'll be flaws that actually MATTER to the character and the story, unlike, say, Bella Swan being so super clumsy but it practically never actually affects her in the story at all, it's just there for the sake of giving her some random flaw.