Deny bonus feat from Flaws

[athelu]

Hello,
I have replaced the Traits/Flaws mechanic in pathfinder to use a custom system where the user must take flaws to be able to gain points to spend on Traits. However, whenever they chose a flaw they gain a bonus feat. This is not how I want this to work

How do i override this behavior? I was thinking that i could add a eval script step to reduce the number of feats available but i have no idea what thing that is.