The first time it is recorded that the people murmured against Moses, after he led them out of bondage, was at Marah, almost immediately after he had led them through the Red Sea (Exodus 15:24-25). They murmured against him, because they had no water, for the water there was bitter. Therefore, Moses sweetened the water. Next, they murmured, because they were hungry and had no food, so the Lord rained bread (manna) from heaven (Exodus 16:2-4, 15; cp. John 6:31). A little later they murmured against him, once again, at a place in Rephidim, which Moses called Massah and Miribah, meaning strife, because the people had no water. Therefore, the Lord had Moses strike a rock in Horeb, and immediately drinking water came forth (Exodus 17:3-7). So, the people murmured over the lack of food and water to sustain life. Whenever they believed their lives were in danger, they murmured against Moses.
In the context of John 6, the people who followed Jesus to the synagogue at Capernaum, believed he was the Prophet who should come (John 6:14). That is, they believed Jesus was the Prophet Moses claimed would be like him (Deuteronomy 18:15-19). This Prophet was supposed to speak for God, and the Lord would demand it of the people who listened to him that they would submit and obey him. While these folks perceived Jesus was this Prophet, and they wished to make him their king (John 6:14), they, nevertheless, almost immediately afterward, murmured against him (John 6:41), because he claimed to be the Bread that has come out of heaven from God to give them life (John 6:38, 40). Suddenly, they thought they were able to see (John 9:40-41), and in seeing they believed they knew him. They claimed that they knew his family (John 6:42), so how could he have come out of heaven from God?
The ancients might just as well have wondered about Moses: “how could this tree make the bitter waters sweet and drinkable?” (cp. Exodus 15:24-25). On the other hand, they could also have said: “how could the heavens rain bread? Really, Moses? You make no sense at all” (Exodus 16:2-4), or they might have told him: “how could water come out of a rock? Even a child knows such a thing is ridiculous” (Exodus 17:3-7). In the context of God doing the works, what good is physical sight or physical understanding? God, who is Spirit (John 4:24), isn’t limited by what is physical. Rather, his worshipers are able to worship him, only if they do so by coming to him in spirit and truth (John 4:24). Therefore, Jesus told these would-be disciples that the words he spoke to them had a spiritual meaning (John 6:63), so don’t try to put them into a physical context. Murmuring against him over what they physically understood or what they were able to see with their own eyes (John 6:42; 9:40-41), made no sense.
Earlier, Jesus told Nicodemus that the Kingdom of God was a spiritual kingdom and couldn’t be seen, unless a man were born again (John 3:3). Nevertheless, even though Nicodemus was an educated ruler of Israel, he didn’t understand Jesus’ spiritual meaning. That is, he had no context for Jesus’ spiritual words (cp. John 3:4). If one is speaking in the spirit, his words seem ridiculous in a physical context. Cursing the darkness won’t make the sun rise. A miracle must take place within one’s heart. One’s whole worldview must be changed, before one is able to see the Kingdom of God, and for that to occur, a man must admit he doesn’t understand, vis-à-vis he must be willing to let God change his worldview and believe Jesus (John 6:28-29). God’s Kingdom cannot be seen with one’s physical eyes, because it is something within the heart of man (Luke 17:20-21; cp. John 3:3). Therefore, to murmur over what one is unable to understand through his five senses is to miss the point of Jesus’ words (John 6:41-42, 63).