Disadvantages
Disadvantages represent a character's foibles and vulnerabilities, and often get shorthanded to flaws (or +flaws). All characters are expected to have a minimum of three flaws; you can have more but it's not necessary. Disadvantages are sorted into three characters, of which you must have at least one of each: Trouble, Significant, Minor. You can also have more than a Minor for the third if desired, but it's not required.
A Trouble is the equivalent of a Defining disadvantage. It should be rooted in your character's personality. It's a way they act that gets them in trouble, and it should be something that can't really be fixed or totally mitigated. If your Trouble can be totally mitigated or ignored, it's not a Trouble. A good example of a Trouble is Marty McFly being baited into doing anything and everything risky when he's called a coward in Back to the Future.
A Significant disadvantage can be anything. It can be another personality deficiency, a physical weakness, etc. It should be, as the name implies, nontrivial.
A Minor disadvantage likewise can be anything.
Non-Flaws
An example of a bad disadvantage, or non-flaw which does effectively nothing:
Hot-Headed Guy: Hero A is a very hot-headed guy. He gets angry easily and rushes his way into problems constantly. However, if he knows someone is trying to make him get angry, he's smart enough to stop himself from getting baited into making these mistakes. He also listens to his allies when they tell him to calm down or they need him to keep an even head for the mission.
Because this flaw explicitly excludes the character getting played, it's not really a flaw. It'd be a great Trouble otherwise.
Theme-Specific Flaws: There are also flaws that only really apply within a specific setting or require their player to go far out of the way to trigger on themselves: Being hunted by some faction or another that nobody plays or will likely ever play, for instance.
Extremely Crippling Flaws: Lastly, there are flaws that are so crippling that people would be uncomfortable invoking them. Being a Matrix character whose body is vulnerable at some off-site location, or having a weak point that instantly defeats you for instance are things that technically read as valid flaws but which won't come up because vanishingly few people are willing to actually do anything with them.
