Finally, Webby's initial screw up catches up with them as the Beagle Boys invade the arcade and capture them. Webby is still in sulk mode and admits that she ruins everything and that she was trying extra hard all day to fit in, her biggest mistake. The boys forgive her and tell her to ease up, and that she doesn't need to force it. At this point Webby's talents become the key to saving the day and redeeming herself.
Now a lot of people look at that and say "fake flaw!" because Webby's initial antics were played off as funny. But they were funny to the audience, for the nephews it was a huge pain. Also, the nephews forgiving her and allowing her to redeem herself, meaning she "gets away with it." Nonsense, she had to admit her mistake and they told her to quit being a spaz. What are you expecting in this kid's cartoon, 40 lashes? No. The audience knew she fucked up, the nephews knew, and Webby herself knew, and she was told how to do better and allowed to fix her mistake. For a Webby focused episode it was a perfect way to play up her faults, force Webby and others to acknowledge them, and then give her a chance to shine and fix what she broke.
So that's why I'm fine with how Webby was handled in her episode, and that's why I accept her flaws as real flaws and not just "her flaw is that she's too perfect and everyone likes her" Mary Sue shit.