I don't think there's any logical conflict. They stated that they thought the type of prion they were handling couldn't infect humans. They see now they were likely wrong.
It immediately goes on to talk about their own discovery 10 years ago that prions could be spread through aerosols which "totally shocked" them and might "warrant re-thinking on prion biosafety guidelines" but that seems an entirely separate thing from the decision to use only sheep prions for research.