So far as I know you could have paid with a credit card. Perhaps the customs agent thought htat it loked new. Unfortunately, many people try to slip things in and this has led to a feeling of an adversary relationship. Contact AACI. They have counselors who help people with these and other issues involving the Israeli system.
BTW, the Americans are no better and even worse. I was asked suspiciously why my passport was issued in Yerushalayim and there was a case where an Israeli couple was expelled for having a picture of the Ben Ish Chai which the customs officials took to be Bin Laden.