Usage patterns
〈人〉の欠点を指摘するto point out someone's flaw
My friend pointed out my flaw to me.
欠点を克服するto overcome a flaw or weak point
He is making an effort to overcome his weaknesses.
〈事〉に欠点があるthere is a flaw in (a plan, system, etc.)
There are a few flaws in this plan.
〈教科〉で欠点をとるto get a failing grade in a subject
I got a failing grade in math.