Why did Jesus ask the disciples why they were troubled and why thoughts were arising in their hearts?
Jesus asked because He could see their inner thoughts and knew they were gripped by fear, doubt, and consternation after His sudden appearance. He exposed their troubled hearts to calm them and to show that, though He had predicted His death and resurrection, those truths had been sovereignly hidden from them until God's appointed time.
Les explains that when Jesus suddenly appeared to the disciples without a door or window, they were naturally shaken, probably half scared to death, so He first said, "Peace be unto you." Yet even with those words of comfort they were terrified and affrighted, supposing they had seen a spirit or ghost. In verse 38 Jesus asked, "Why are you troubled? Why do thoughts arise in your hearts?" Les points out that Jesus could look right through their thinking and saw their thoughts of consternation, fear, and doubt. He was addressing what was going on inside them, asking in effect, "What's the matter with you fellows?" The context shows they had been with Him three years, and He had told them in Luke 18 that He would go to Jerusalem, be scourged, beaten, spit on, crucified, and rise the third day. But the next verse says they understood none of those things; it was hidden from them providentially and sovereignly. Les applies the same principle here: they should have known, but God had providentially hidden these things until the time He ordained that they understand. So Jesus' question exposed both His knowledge of their hearts and their need to be settled and taught.
And he said unto them, Why are ye troubled? and why do thoughts arise in your hearts?