At his weekly Motzei Shabbos Shiur, Chacham Ovadia Yosef Shlita warned that people should use caution when doing Kapporos with chickens. His concern is that a Shochet who is Shechting thousands of chickens, can be using a Chalif (knife) which may not be perfectly smooth – making the chicken Treif.
He also mentioned the Mechaber in Shulchan Aruch who says that “one should refrain from doing Kapporos – just to bring out his strong warning. He called on those who wish to perform the Kapporos Minhag with a chicken to do so early to prevent overloading the Shochtim, and “also to go to Shochtim who are Yirei Shomayim.”
NOTE: Even though the Mechaber in Shulchan Aruch makes that statement regarding the Minhag of Kapporos, it must be noted that Sephardim still in fact do the Minhag Kapparos.