According to TMZ, the Miss Universe Organization sent a cease and desist order to NOM, demanding they stop playing their anti-gay ad featuring Miss CA.
Because the ad contains footage of the Miss USA pageant when Miss CA Carrie Prejean gives her infamous response against marriage equality. By using that footage, the organization claims NOM is violating copyright law.
Though they claim they're not taking sides on the issue, they are claiming they don't want to the footage to support NOM's agenda.
It's a fine line they're walking, and they have stated they don't approve of Miss CA's anti-gay response on their show. I say this is a smart move. Otherwise, they would offend half of their employees - gay men.