I've ALWAYS seen the contradiction! If Jesus started the CATHOLIC Church, He wouldn't be chastising it before the bible was even finished!!
Paul chastised every one of the local churches he planted ("You foolish Galatians!") --- and he had a whole LOT of rebuke for the Corinthians. He brings their divisions right out in front of their faces, tells them how much he has worried over them, prayed for them, wept for their sake--- and do they appreciate the necessary correction? It seems questionable at times: "Though the more abundantly I love you, the less I be loved" (II Cor. 12:15).
But does he ever say "Leave that church"? Nope.
He understands that you struggle for the Bride of Christ. You don't kick her to the curb.