The Bible does not airbrush doubt. Thomas refused to believe the resurrection without physical evidence, and Jesus came back a week later specifically for him — not to rebuke him, but to show him the wounds. Jesus didn't say "you should have believed anyway." He said "reach hither thy hand." The invitation to honest examination is inside the resurrection story, not a departure from it.
Peter denied Jesus three times on the night of the arrest. He swore with curses that he didn't know the man. Three days later Jesus appeared to him on the beach and asked the same question three times: "Simon, son of Jonas, lovest thou me?" Once for each denial. Jesus reconstructed what Peter had destroyed — not by pretending the betrayal didn't happen, but by addressing each instance directly. Restoration required naming the thing that broke.
The man in Mark 9 comes to Jesus with a demon-possessed son and says "if thou canst do any thing, have compassion on us, and help us." Jesus corrects the if — "all things are possible to him that believeth" — and the man's response is one of the most honest things anyone ever said to Jesus: "Lord, I believe; help thou mine unbelief." Jesus healed the boy. The mixed prayer — belief and unbelief together, in the same breath — was enough. Scripture did not require the unbelief to be resolved before Jesus acted.
Commentary is from a charismatic Protestant perspective, drawing on KJV text and public-domain sources including Spurgeon, Andrew Murray, and Matthew Henry.