No problem with my Comptech CAI. Sounds like you don't have the housing or the intake tube placed properly. One of the hood buttons does contact the carbon fiber cover.

 

I have the same problem with my Comptech airbox and carbon fiber hood rubbing the top of the box and leaving a little white rub mark there. I don't really sweat it but I guess I'd like it fixed...no one else has this problem?

 

They pretty much all rub.