Here are a few methods, up to you which you like to use!

The Flaw Roulette:
You get a big ol’ list of flaws, and then you pick at random. Throw darts, scroll and pick, whatever you like.
+ : Great way to get your imagination moving as an exercise, creates unique, unusual character mixes.
- : Sometimes all the traits just don’t blend. Good writing can usually cover you here, but some can be an extra challenge.
A few such lists (Please note that not all have read my previous post. Damn shame, but. Salt before reading): 
One
Two
Three

Next on the table is the Yin Yang or Everything Varies method:
In which all traits (positive, negative, and neutral) can be a strength or a weakness, and vary depending upon the situation. Ex., your character is ‘assertive’. On a good day, they calmly tell some bullies to leave them alone. Great. On a bad day, they snap at and embarrass a shy person who tried to make a joke about them but failed. Not great. 
+: Logical and lifelike way of representing your character’s personality. Seems realistic because people are usually ranged like that. 
- : A little harder to be creative with, and sometimes you have to think about how a normally positive trait could cause problems, or how a negative trait could be helpful.  

The Worst Possible Thing:
aka Tragic Flaw, or Screwing Them Over By Design.
In which you pick a flaw that will be the absolute worst thing you can do to them- that will get them in trouble or cause them to fall. A staple of the Tragic Hero archetype, in which hubris is favored.
+: Great literature often can be made by finding creative ways to totally ruin your character. Good for creating a sympathetically flawed character.
- :  It can give a sense of fate acting in your story rather than the character’s choices messing them up, because they’re screwed over so badly. 

Enjoy. :)
-Evvy