If you leave out the bolded part I agree with you but I think he paused because he was genuinely surprised to learn Jon said that. He doesn't really indicate that he or the UFC knew anything about a failed test before the fight.
He definitely goes into dana damage control mode but it didn't seem flustered or at a loss to me. He just seemed genuinely surprised Jon made the claim.
It doesn't really matter though. The goof tells plenty of lies so I will concede it is entirely possible you are correct but I just didn't really see it here. It's possible you are right that they knew of the failed test and stuck vitor in there anyway but he didn't really seem flustered by the question, more confused by the new information and trying to make sense of how Jon could be a source for that claim.
It's fuckin' weird to be sorta-kinda defending dana. Stop making me do it. Go away!