So, your only problem is not being able to give 'bad' personality traits to your characters?
It doesn't have to be a big flaw. It can be done in a subtle way.
Here are some negative personality traits:
* distant, cold, aloof
* self-satisfied, unmotivated
* closed, guarded, secretive
* uncaring, unfeeling, callous
* cheerless, gloomy, sour, grumpy
* inconsiderate, thoughtless
* uncooperative, unhelpful, combative
* rude, impolite
* uncommitted, uncaring, hostile
* indecisive, unsure
* relents, gives up
* inflexible, rigid, unbending, stubborn
* ill-will, malice, hatred
* dishonest, deceiving, lying
* arrogant, conceited, ego-centric
* jealous, envious, covetous
* pretentious, affected, ostentatious
So, for example..
You cannot have your character 'Hard-working' and 'Lazy' at the same time.
Another tip is to focus on the people around you, actors/actresses on television and characters from books you've enjoyed. Which ones do you think have a good personality? Why?
That can be your starting point in finding your OWN character personalities.