They have a program to facillitate regular border crossing. They fingerprint and do an FBI background check on you and any family members under eighteen. Once you are cleared, they give you a sticker for your car and you are allowed to cross the border at will, but you cannot take anyone with you that is not on your family list. If you are caught taking non-approved people across with you, you are in big trouble. This is probably what was going on with these Muslims.
Then it would be very simple to say that's why they were further investigated. Since the CBP officers did not give that as their justification for it, then I suspect it's not the case. Are you just speculating, or do you have info beyond what was reported?